A simple question

[renjincomeon]

What does "$2" in section 6.1 mean. Please don't laugh at me, I am a novice.

seacr="/fh/fast/gottardo_r/yezheng_working/Software/SEACR/SEACR_1.3.sh"
histControl=$2
mkdir -p $projPath/peakCalling/SEACR

[yezhengSTAT]

Sorry for the confusion, it does look weird using $2 here. We can use variable=$1 anotherVariable=$2 to pass parameters when running the shell scripts, for example, bash somescript.sh variable1 variable2. Please just give this variable, histControl, IgG sample name to specify the IgG file used as a control in peak calling.

Hello Ye, thank you for this pipeline. I have a question about SEACR.

Are you using the same IgG file as control in peak calling ?

Or one IgG replicate for one replicate of H3K4me3 and one of H3K27me3 and the other IgG replicate for the second replicate of H3K4me3 and H3K27me3 ?

Thank you very much in advance for your answer,
Morgane

[yezhengSTAT]

Hello Morgane,
If you have the matching IgG control for one specific replicate of K4me3/K27me3, it makes more sense to use the matching one to ensure same background landscape of K4me3/K27me3 and the background captured by IgG.

Thanks,
Ye

[MarionPerrier]

Hi Ye !

Thank you a lot for this very interesting tutorial.
I have a question regarding the part 7.2.1, using computeMatrix : Is hg38_gene.tsv just a simple list of genes features ?
In the documentation of computeMatrix scale-regions, it is indicated to use a .bed or .gtf file after the -R argument, so I am a bit confused.

Have a good day,
Marion

[yezhengSTAT]

Hi Ye !

Thank you a lot for this very interesting tutorial. I have a question regarding the part 7.2.1, using computeMatrix : Is hg38_gene.tsv just a simple list of genes features ? In the documentation of computeMatrix scale-regions, it is indicated to use a .bed or .gtf file after the -R argument, so I am a bit confused.

Have a good day, Marion

Hello Marion,
Thanks for your interest in this tutorial!

Apologize that it is probably better to rename the file to hg38_gene.bed because it is basically a bed file containing the regions of the genes. I believe I directly downloaded it from the UCSC genome browser. I am attaching a snapshot of the file content below.

chr1	11868	14409	ENST00000456328.2	0	+	11868	11868	0	3	359,109,1189,	0,744,1352,
chr1	14403	29570	ENST00000488147.1	0	-	14403	14403	0	11	98,34,152,159,198,136,137,147,99,154,37,	0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130,
chr1	17368	17436	ENST00000619216.1	0	-	17368	17368	0	1	68,	0,
chr1	29553	31097	ENST00000473358.1	0	+	29553	29553	0	3	486,104,122,	0,1010,1422,
chr1	30365	30503	ENST00000607096.1	0	+	30365	30365	0	1	138,	0,
chr1	34553	36081	ENST00000417324.1	0	-	34553	34553	0	3	621,205,361,	0,723,1167,
chr1	52472	53312	ENST00000606857.1	0	+	52472	52472	0	1	840,	0,
chr1	57597	64116	ENST00000642116.1	0	+	57597	57597	0	3	56,157,1201,	0,1102,5318,
chr1	69054	70108	ENST00000335137.4	0	+	69090	70008	0	1	1054,	0,
chr1	89294	120932	ENST00000466430.5	0	-	89294	89294	0	4	2335,150,105,158,	0,2796,23405,31480,

Thanks,
Ye

[Yolanda233]

Hello ,ye! Thanks for sharing this pipeline! I've run this pipeline successfully using data you prepared. However, when I try to run my own cuttag data(transcript factor), something goes wrong. Specificly, one of my IgG replication has none of reads that can align to E.coli genom. This results my spike-in calibration going wrong. Do you have any idea about this situation? or do you have any recomandation?