Hi all, I want to run the chipseq pipeline on this dataset. According to the documentation, the read_length has to be in [50, 75, 100, 150, 200]. Nonetheless, the reads in the fastqs I downloaded from GEO are 44bp long:

@SRR3440073.51722 HWI-ST665_0114:3:1101:4300:7105/1
TTTCCTGTTGAAGTGAGGTTTTGCTATGCTTTCACCTCACATAC
+
CCCFFFFFHHHHHHJJJJFHIJJJJJJJJJJJJJJJJJJJJJJJ
@SRR3440073.51723 HWI-ST665_0114:3:1101:4431:7108/1
GAAAGGACTGGAATGGAATGGAATGGAATGGAATGGAATCAACT
+
CBCFFFFFHHHHHJJJJJJJJJJJJJIJJJJIJJJJIJJJIIIJ
@SRR3440073.51724 HWI-ST665_0114:3:1101:4454:7115/1
CCAGGCTGGAGTGCAATGGCACGATCTGGGCTCACTGCAACCTC
+
@@CFFDFDDFFHHIJJGGIIJIGJIJJIJIIGGHIFGEIIIJGH
@SRR3440073.51725 HWI-ST665_0114:3:1101:4376:7119/1
TTCGATGATGATTCCATTCATTTCCATCCCATGATGATTCCATT
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJ
@SRR3440073.51726 HWI-ST665_0114:3:1101:4335:7138/1
TGCCTGGGATTTCACTCTGAGCCTTGGCTTTTCAGTGGCCCAGT
+
@@CFDFDFHHHFHIHHIJIHGEGHIJIGGIGIIJGGHIGIJEHB

How should I set this parameter in my case? thank you!

Hi, this is because we provide pre-compiled values for

macs_gsize

as you can see on this example but you can provide it directly using the

--macs_gsize

parameter, see the docs for --macs_gsize and --read_length