#Genome awk -f filter-annotation_e.awk mm10b.gtf > mm10e.gtf Kept 1461866 annotations, dropped 29684 awk -f get-biotype-stats.awk mm10e.gtf 3prime_overlapping_ncrna 3 nonsense_mediated_decay 4912 TR_D_gene 5 ribozyme 22 misc_RNA 566 Mt_rRNA 2 rRNA 354 antisense 2997 non_stop_decay 13 retained_intron 15621 sense_overlapping 44 sRNA 2 lincRNA 5094 processed_transcript 13444 miRNA 2202 sense_intronic 259 TEC 1962 protein_coding 49676 macro_lncRNA 2 snRNA 1382 awk -f get-gene-lengths2.awk mm10e.gtf > mm10e.gene-lenghts.txt # cd /mnt/max/b/genomics_facility/DKlab/mr/tzanos/rep/e/RNAseq /data/results/tools/rnaseq/subread/subread-2.0.0-source/bin/featureCounts -O -g "gene_id" -t exon -T 8 -a /home/tzanos/Desktop/biotype-annotated_genome/mm10e.gtf -o gene_counts_merged_k20_mm10e.txt /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wt01_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wt02_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wt21_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wt22_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wt61_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wt62_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wtIFN_1_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wtIFN_2_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wtIL4_1_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/wtIL4_2_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KO01_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KO02_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KO21_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KO22_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KO61_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KO62_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KOIFN_1_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KOIFN_2_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KOIL4_1_trm_k20.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/rnaseq/bam/KOIL4_2_trm_k20.bam ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.0 //========================== featureCounts setting ===========================\\ || || || Input files : 20 BAM files || || o wt01_trm_k20.bam || || o wt02_trm_k20.bam || || o wt21_trm_k20.bam || || o wt22_trm_k20.bam || || o wt61_trm_k20.bam || || o wt62_trm_k20.bam || || o wtIFN_1_trm_k20.bam || || o wtIFN_2_trm_k20.bam || || o wtIL4_1_trm_k20.bam || || o wtIL4_2_trm_k20.bam || || o KO01_trm_k20.bam || || o KO02_trm_k20.bam || || o KO21_trm_k20.bam || || o KO22_trm_k20.bam || || o KO61_trm_k20.bam || || o KO62_trm_k20.bam || || o KOIFN_1_trm_k20.bam || || o KOIFN_2_trm_k20.bam || || o KOIL4_1_trm_k20.bam || || o KOIL4_2_trm_k20.bam || || || || Output file : gene_counts_merged_k20_mm10e.txt || || Summary : gene_counts_merged_k20_mm10e.txt.summary || || Annotation : mm10e.gtf (GTF) || || Dir for temp files : ./ || || || || Threads : 8 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : not counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file mm10e.gtf ... || || Features : 670148 || || Meta-features : 35095 || || Chromosomes/contigs : 22 || || || || Process BAM file wt01_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 95809333 || || Successfully assigned alignments : 71606150 (74.7%) || || Running time : 0.25 minutes || || || || Process BAM file wt02_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 98012748 || || Successfully assigned alignments : 72350806 (73.8%) || || Running time : 0.26 minutes || || || || Process BAM file wt21_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 90535758 || || Successfully assigned alignments : 67173575 (74.2%) || || Running time : 0.24 minutes || || || || Process BAM file wt22_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 107217949 || || Successfully assigned alignments : 77566241 (72.3%) || || Running time : 0.28 minutes || || || || Process BAM file wt61_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 105671339 || || Successfully assigned alignments : 77263154 (73.1%) || || Running time : 0.28 minutes || || || || Process BAM file wt62_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 101789242 || || Successfully assigned alignments : 74611443 (73.3%) || || Running time : 0.27 minutes || || || || Process BAM file wtIFN_1_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 105895532 || || Successfully assigned alignments : 76419358 (72.2%) || || Running time : 0.28 minutes || || || || Process BAM file wtIFN_2_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 140533258 || || Successfully assigned alignments : 101738781 (72.4%) || || Running time : 0.37 minutes || || || || Process BAM file wtIL4_1_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 124190875 || || Successfully assigned alignments : 89449210 (72.0%) || || Running time : 0.34 minutes || || || || Process BAM file wtIL4_2_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 94945834 || || Successfully assigned alignments : 68720108 (72.4%) || || Running time : 0.26 minutes || || || || Process BAM file KO01_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 107505222 || || Successfully assigned alignments : 78167559 (72.7%) || || Running time : 0.28 minutes || || || || Process BAM file KO02_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 134698963 || || Successfully assigned alignments : 99492500 (73.9%) || || Running time : 0.35 minutes || || || || Process BAM file KO21_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 130372666 || || Successfully assigned alignments : 94949177 (72.8%) || || Running time : 0.34 minutes || || || || Process BAM file KO22_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 128757909 || || Successfully assigned alignments : 94155471 (73.1%) || || Running time : 0.33 minutes || || || || Process BAM file KO61_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 123118006 || || Successfully assigned alignments : 90185875 (73.3%) || || Running time : 0.32 minutes || || || || Process BAM file KO62_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 146957015 || || Successfully assigned alignments : 106676604 (72.6%) || || Running time : 0.39 minutes || || || || Process BAM file KOIFN_1_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 135561836 || || Successfully assigned alignments : 99181458 (73.2%) || || Running time : 0.36 minutes || || || || Process BAM file KOIFN_2_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 117903198 || || Successfully assigned alignments : 86015148 (73.0%) || || Running time : 0.32 minutes || || || || Process BAM file KOIL4_1_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 134655139 || || Successfully assigned alignments : 98404687 (73.1%) || || Running time : 0.37 minutes || || || || Process BAM file KOIL4_2_trm_k20.bam... || || WARNING: Paired-end reads were found. || || Total alignments : 138357739 || || Successfully assigned alignments : 100929817 (72.9%) || || Running time : 0.38 minutes || || || || || || Summary of counting results can be found in file "gene_counts_merged_k20_ || || mm10e.txt.summary" || || || \\============================================================================// # cd /mnt/max/b/genomics_facility/DKlab/mr/tzanos/rep/e/PolysomeSeq /data/results/tools/rnaseq/subread/subread-2.0.0-source/bin/featureCounts -O -g "gene_id" -t exon -T 8 -a /home/tzanos/Desktop/biotype-annotated_genome/mm10e.gtf -o gene_counts_merged_mm10e.txt /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_0h_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_0h_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_2h_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_2h_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_6h_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_6h_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_IFN-gamma_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_IFN_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_IL4_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/KO_IL4_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_0h_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_0h_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_2h_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_2h_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_6h_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_6h_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_IFN-gamma_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_IFN-gamma_replicate_Ib/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_IL4_replicate_IIb/accepted_hits.bam /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/polysomeseq/bam/WT_IL4_replicate_Ib/accepted_hits.bam ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.0 //========================== featureCounts setting ===========================\\ || || || Input files : 20 BAM files || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || o accepted_hits.bam || || || || Output file : gene_counts_merged_mm10e.txt || || Summary : gene_counts_merged_mm10e.txt.summary || || Annotation : mm10e.gtf (GTF) || || Dir for temp files : ./ || || || || Threads : 8 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : not counted || || Multi-overlapping reads : counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file mm10e.gtf ... || || Features : 670148 || || Meta-features : 35095 || || Chromosomes/contigs : 22 || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 7521987 || || Successfully assigned alignments : 838147 (11.1%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 6544845 || || Successfully assigned alignments : 721552 (11.0%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 9159393 || || Successfully assigned alignments : 700147 (7.6%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 7386589 || || Successfully assigned alignments : 637578 (8.6%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 7746546 || || Successfully assigned alignments : 624419 (8.1%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 9381660 || || Successfully assigned alignments : 866682 (9.2%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 7813278 || || Successfully assigned alignments : 737843 (9.4%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 11018317 || || Successfully assigned alignments : 983984 (8.9%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 5585330 || || Successfully assigned alignments : 535285 (9.6%) || || Running time : 0.01 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 6679500 || || Successfully assigned alignments : 714450 (10.7%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 3839289 || || Successfully assigned alignments : 388051 (10.1%) || || Running time : 0.01 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 6359156 || || Successfully assigned alignments : 613149 (9.6%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 4598368 || || Successfully assigned alignments : 325562 (7.1%) || || Running time : 0.01 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 6335425 || || Successfully assigned alignments : 651780 (10.3%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 5569597 || || Successfully assigned alignments : 694053 (12.5%) || || Running time : 0.02 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 3745813 || || Successfully assigned alignments : 442654 (11.8%) || || Running time : 0.01 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 5769482 || || Successfully assigned alignments : 564873 (9.8%) || || Running time : 0.01 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 4539599 || || Successfully assigned alignments : 664868 (14.6%) || || Running time : 0.01 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 3351295 || || Successfully assigned alignments : 531907 (15.9%) || || Running time : 0.01 minutes || || || || Process BAM file accepted_hits.bam... || || Single-end reads are included. || || Total alignments : 4817805 || || Successfully assigned alignments : 777858 (16.1%) || || Running time : 0.01 minutes || || || || || || Summary of counting results can be found in file "gene_counts_merged_mm10 || || e.txt.summary" || || || \\============================================================================//