#@ 'correct' metaseqR by P.Moulos (2014):
samplename	filename	condition	paired	stranded
SCR10-E145-4wt	/media/raid/tmp/fck/cer/SCR10-E145-4wt.bam	WT	single	yes
SCR12-E145-6Het	/media/raid/tmp/fck/cer/SCR12-E145-6Het.bam	Het	single	yes
SCR13-E145-3wt	/media/raid/tmp/fck/cer/SCR13-E145-3wt.bam	WT	single	yes
SCR15-E145Het7	/media/raid/tmp/fck/cer/SCR15-E145Het7.bam	Het	single	yes

#@

Dear Silvia,

to clarify what has been done up to now
I list all sample IDs in all sequencing runs we have made.
The IDs are unique. If there are any mistakes (e.g. for SCR21 and SCR22)
or missing information (e.g. 'P1' is missing in all IDs),
please edit this list
so we can sort the results.

BW,
Martin


run20
SC1_E15.5_1-3
SC2_E15.5_2-4

run106
SCR10-E145-4wt
SCR12-E145-6Het

run107
SCR13-E145-3wt
SCR14-E145-5Het

run118
SCR15-E145HET7 R_2014_12_02_12_33_41_user_ION-118-SCereghini_RNAseq_SCR15-ITlab-ChIP_ITC38-42-43_141202.SCR15.IonXpressRNA_016.fastq.gz
  
run127
SCR16r-65n2mut
SCR18r-65n8wt
DrSCereghini_4RNAseq_SCR16r-65n2mut-bc2_SCR18r-65n8wt-bc5

run128
SCR17r-65n5mut
SCR19r-65n11wt

run141
SCR21-7wt
SCR23-8Het

run143
SCR20-6wt
SCR22-5Het

run299 (3UTRseq)
SC3R1-1M14 	
SC3R2-3M14 	
SC3R3-6M14mut 	
SC3R4-8M14mut 	
SC3R5-9M14mut 	
SC3R6-1F16 	
SC3R7-6F16 	
SC3R8-2F16mut 	
SC3R9-5F16mut 	
SC3R10-8F16mut 	







/data/images/proton/run107/samples.txt
Barcode Name	Sample	Bases	>=Q20 Bases	Reads	Mean Read Length
No barcode	None	192705514	163397304	1823405	105 bp 
IonXpressRNA_002	SCR13	6700709168	6013307709	72340797	92 bp 
IonXpressRNA_010	SCR14	1675181557	1492520215	14801845	113 bp 
DrSCereghini_4RNAseqsamples_SCR13-E145-3wt-bc2_SCR14-E145-5Het-bc10_SCR14 has been repurified 141104 

/data/images/proton/run128/samples.txt
Barcode Name	Sample	Bases	>=Q20 Bases	Reads	Mean Read Length
No barcode	None	192809390	147479497	1452991	132 bp 
IonXpressRNA_004	SCR17r	7280977907	5891911959	50831051	143 bp 
IonXpressRNA_015	SCR19r	4957738983	4040853945	35550931	139 bp 
DrSCereghini_4RNAseq_SCR17r-65n5mut-bc4_SCR19r-65n11wt-bc15

/data/images/proton/run141/samples.txt
Barcode Name	Sample	Bases	>=Q20 Bases	Reads	Mean Read Length
No barcode	None	203149442	148050060	2273612	89 bp 
IonXpressRNA_005	SCR20-6wt	5291689056	4457739280	46440376	114 bp 
IonXpressRNA_014	SCR22-5Het	3402202041	2937307254	36657973	93 bp 
DrSCereghini_4RNAseq_SCR20-6wtt-bc5_SCR22-5Het-bc14 

/data/images/proton/run143/samples.txt
Barcode Name	Sample	Bases	>=Q20 Bases	Reads	Mean Read Length
No barcode	None	135771582	101334477	1483666	92 bp 
IonXpressRNA_009	SCR21-7wt	4539420375	3895138980	38446150	118 bp 
IonXpressRNA_015	SCR23-8Het	6367014349	5334979798	47146473	135 bp 
DrSCereghini_4RNAseq_SCR21-7wt-bc9_SCR23-8Het-bc15

run299
	Read Length Histogram 	Files
No barcode 	None 	978,168,943 	765,971,089 	8,254,988 	118 bp 		UBAM BAM BAI
IonXpress_001 	SC3R1-1M14 	754,697,994 	597,392,981 	6,710,396 	112 bp 		UBAM BAM BAI
IonXpress_002 	SC3R2-3M14 	527,791,920 	418,455,318 	4,694,087 	112 bp 		UBAM BAM BAI
IonXpress_003 	SC3R3-6M14mut 	496,461,424 	396,215,004 	4,350,420 	114 bp 		UBAM BAM BAI
IonXpress_004 	SC3R4-8M14mut 	432,029,510 	345,246,424 	3,935,188 	110 bp 		UBAM BAM BAI
IonXpress_005 	SC3R5-9M14mut 	532,860,451 	423,487,141 	4,735,942 	113 bp 		UBAM BAM BAI
IonXpress_006 	SC3R6-1F16 	427,300,477 	335,264,669 	3,658,897 	117 bp 		UBAM BAM BAI
IonXpress_007 	SC3R7-6F16 	449,601,650 	353,769,914 	3,813,600 	118 bp 		UBAM BAM BAI
IonXpress_008 	SC3R8-2F16mut 	630,829,776 	500,084,022 	5,693,795 	111 bp 		UBAM BAM BAI
IonXpress_009 	SC3R9-5F16mut 	513,269,492 	408,979,910 	4,434,506 	116 bp 		UBAM BAM BAI
IonXpress_010 	SC3R10-8F16mut 	525,157,166 	412,182,876 	4,954,907 	106 bp 		UBAM BAM BAI




/data/images/proton/Cereghini/run142/metaseqr_wt_vs_mut_run142/index.html
<strong>Conditions:</strong> WT, HET</br>
                                    <strong>Samples:</strong> SCR20, SCR21, SCR22, SCR23</br>

/data/images/proton/Cereghini/run142/metaseqr_wt_vs_het_run142_woSCR22/index.html
<strong>Conditions:</strong> WT, HET</br>
                                    <strong>Samples:</strong> SCR20, SCR21, SCR23</br>

The negative log2(fold_change) in 
Cereghini/Tuxedo_run143/gene_exp.diff
are cmoparable with the log2_normalized_fold_change_WT_vs_HET in
Cereghini/run142/metaseqr_wt_vs_het_run142_woSCR22/lists/metaseqr_sig_out_WT_vs_HET.txt.gz

/data/images/proton/Cereghini/run142/metaseqr_wt_vs_het_run142_woSCR22-scr21_wt_instead_of_het/index.html
                                    <strong>Conditions:</strong> WT, HET</br>
                                    <strong>Samples:</strong> SCR20, SCR21, SCR23</br>

/data/images/proton/run143/www/tuxedo/cuffdiff_HET_vs_WT/run.info
param	value
cmd_line	cuffdiff -L HET,WT --no-length-correction --library-type fr-secondstrand --no-update-check --num-threads 10 -q -o cuffdiff_HET_vs_WT merged_asm/merged.gtf RCAD_P1_HET_SCR23.bam2 RCAD_P1_WT_SCR20.bam2,RCAD_P1_WT_SCR21.bam2 
version	2.2.1