/data/images/proton2/run373/PRDM16reczko@max:/data/images/proton2/run373/PRDM16$ /data/results/tools/blast/ncbi-blast-2.2.25+/bin/makeblastdb -in prdm16.fa  -parse_seqids -dbtype nucl
reczko@max:/data/images/proton2/run373/PRDM16$ awk '{print ">"substr($0,2);getline;print $0; getline;getline;}' ../R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R3-Tbctrl4.IonXpress_003.fastq > 4C_lincPRDM16.fa
head -4 4C_lincPRDM16.fa | /data/results/tools/blast/ncbi-blast-2.2.25+/bin/blastn -num_threads 1 -evalue 6 -max_target_seqs 10 -outfmt 6 -db nr

#sw alignment
/data/results/tools/align/fasta/fasta-36.3.8f/doc/../bin/map_db -n prdm16.fa
/data/results/tools/align/fasta/fasta-36.3.8f/bin/fasta36 -U -f 9999 4C_lincPRDM16.fa prdm16.fa > 4C_lincPRDM16.aln

/data/results/tools/align/fasta/fasta-36.3.8f/bin/fasta36 -U -f 9999  t/xab prdm16.fa | awk -f /data/images/proton2/run373/PRDM16/fasta2tabfilt.awk > 4C_lincPRDM16b.aln


#bt2
/data/results/tools/align/bowtie2-2.2.9/bowtie2-build-s  prdm16.fa prdm16

time /data/results/tools/align/bowtie2-2.2.9/bowtie2 -p 6 --local --very-sensitive-local  -x prdm16 -U ../R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R3-Tbctrl4.IonXpress_003.fastq  | grep lncPRDM16 > 4C_lincPRDM16.bt2.sam

2CG5G:05771:09234	0	lncPRDM16	1	22	40M16S	*	0	0	GGAGGAAGTCCGTGAGGATCCATCACTTCACGAGCTGCCGGGCAGTGGGCTGCGAG	=9==9=8<<=9==>>A;??8*///--((*(((****9838A39997770///74-*	AS:i:40	XN:i:0	XM:i:9	XO:i:0	XG:i:0	NM:i:9	MD:Z:20A0G0G0G0G1C0C1G1C8	YT:Z:UU
2CG5G:10440:11127	0	lncPRDM16	1	22	41M14S	*	0	0	GGAGGAAGTCCGTGAGGATCATGGGAGCAGTCCGGTGCCGCTTTGACGATGGCGT	<6:;6;8<==6<988;67///9991/////7737)555/55/6///.7...)...	AS:i:46	XN:i:0	XM:i:7	XO:i:0	XG:i:0	NM:i:7	MD:Z:21G3C0C1C1C1A1C6	YT:Z:UU
2CG5G:04432:14273	0	lncPRDM16	1	22	42M42S	*	0	0	GGAGGAAGTCCGTGAGGATCTGAGTCCCAGCCTTCGGCCTCCCAAATGCTGTAATTACACGGCGTCGATGACTGCCGTAACAGG	=9=>9=9==<9@<><=9<=6;+***44,***(*(,6262677*55*58887:9363,,,,,044,.......88838..).440	AS:i:46	XN:i:0	XM:i:8	XO:i:0	XG:i:0	NM:i:8	MD:Z:20A1G1G3C3A0G1T3G2	YT:Z:UU
2CG5G:02202:11696	0	lncPRDM16	1	22	43M1S	*	0	0	GGAGGAAGTCCGTGAGGATCTCGGCTCACGTCAGCTTCTGCCAC	=9==9=9>B>9==<<>7;870//)-///7///9555/555/)//	AS:i:45	XN:i:0	XM:i:8	XO:i:0	XG:i:0	NM:i:8	MD:Z:20A0G2G0C1C2C5G1C4	YT:Z:UU
2CG5G:06208:00464	0	lncPRDM16	1	22	44M18S	*	0	0	GGAGGAAGTCCGTGAGGATCATCGGCTTCACTAGCAGCCTCCAGCATCCCGGGCTCAAAACG	<9<=9@9===9<=>>?9=>=7755488)/--------7)55488:888<4;;*76....(./	AS:i:45	XN:i:0	XM:i:8	XO:i:0	XG:i:0	NM:i:8	MD:Z:21G0G3C0C1G1C3T3G4	YT:Z:UU
2CG5G:01756:13704	0	lncPRDM16	1	22	46M39S	*	0	0	GGAGGAAGTCCGTGAGGATCAGAAGCCTAACCAGTTACAGCCGGTGGACAACTCGTACTAATTTCCCTACAGATGGGTAGCAGGG	;9<>9?9===9<<>==7<<8---2**(*-)-)-//28;:::7;6:87::<5777666///47<2>>3<:;555766)....677/	AS:i:46	XN:i:0	XM:i:9	XO:i:0	XG:i:0	NM:i:9	MD:Z:22G0G3C0C0G4C1G1C3A3	YT:Z:UU
2CG5G:09981:06485	0	lncPRDM16	1	22	47M64S	*	0	0	GGAGGAAGTCCGTGAGGATCTGTGGCCAGGACAGCCGGAGCAGGTGCTGTGGTACAGTGGGGCAGCCACGAGGTGGGCAGGACACAGCGTTGCCATCACCAAGACGACGGT	=9<>9<<?>>;>>B??9><99444.4(**(****,),0488//)/68::8817;;764;<<08744.48844-488079829<888<:::/7529;<<<7<7:::755:28	AS:i:47	XN:i:0	XM:i:10	XO:i:0	XG:i:0	NM:i:10	MD:Z:20A1G4C0C1C4T1C0C2C0A4	YT:Z:UU
2CG5G:10289:07366	0	lncPRDM16	1	22	49M35S	*	0	0	GGAGGAAGTCCGTGAGGATCATCGCCTCAACCAACTGCATCCAGTGCCTCTCCCCCAAGATACAGGTAGGGGGGACAAGCCCAA	@9==9=9===;=BC<<7::7----*(*--)-294677////)///5538879:::'4.4443:8848444444%477)...).1	AS:i:56	XN:i:0	XM:i:9	XO:i:0	XG:i:0	NM:i:9	MD:Z:21G0G1G1C1C0G3G4C0G9	YT:Z:UU

2CG5G:09641:01262	0	lncPRDM16	1	22	28M203S	*	0	0	GGAGGAAGTCCGTGAGGATCAGGGGCCCTAGAATCAGAGAAGTTAAGTCACTTACCTTAGGCCACACAGCTAATAGGTGACAGAGCTAGTCTTTACTTTGAAAATGCTTCTGACAATTCTGAAAACATGCCCAAAGTCCAGTGGAAAGTTATGTTCACTAAATACAACGGTACAGGTGGGGGCAGCCACGAGGTGGGCAGGACACAGCGTTGCCATCACCAAGACGACGGT	/)//)/)/9:4:;<<<5<::9999)8:2::<<7=====<=9>>=>9===<<?8<=9?<?>9>;==>>===<<7<<=9=>@>;;<<<=?;;;<<6<=>?68888.8<<=9=>=:;:7<6<<8:::1:788<>4;:6:<<8<<<9698066)..6638;===>9=<<<8<<9=<<;;5;==>=1:::>7<<<;<6666+6::78::;<::.-(-.066:..).*.9:<><>5<	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YT:Z:UU



/data/results/tools/align/bowtie2-2.2.9/bowtie2 -p 6  -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome /data/images/proton2/run373/R_2017_12_01_12_13_27_user_IONAS-373-DrKobold_PHlab_171201_SK3R-PH4C.SK3R3-Tbctrl4.IonXpress_003.fastq  | samtools view -Sb - | samtools sort -o - - > 4C_PRDM16.bam
samtools index !$

]0;/data/images/proton2/run373/PRDM16reczko@max:/data/images/proton2/run373/PRDM16$ awk -f ../../make-unstranded-sampled-hg38-tracks1.awk  reads.txt  > make-unstranded-sampled-hg38-tracks.sh
]0;/data/images/proton2/run373/PRDM16reczko@max:/data/images/proton2/run373/PRDM16$ source !$
source make-unstranded-sampled-hg38-tracks.sh

/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh 4C_PRDM16.bam /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome 1