PureClip to analyze CLIP-SEQ

Question

[Kai_Qi]

Hi All:

I am doing CLIP-seq analysis following the manual of PureCLIP: I have 2 problems which I can not solve so far:

1 getting the reference genome:

(base) [caiqi@midway2-login2 genome_fa]$ gunzip ref.GRCh38.fa.gz  

gzip: ref.GRCh38.fa.gz: unexpected end of file
(base) [caiqi@midway2-login2 genome_fa]$ zcat ref.GRCh38.fa.gz > ref.GRCh38.fa

gzip: ref.GRCh38.fa.gz: unexpected end of file

So I tried to get the reference genome from the iGenome website to do the STAR mapping and other preprocessing. Everything goes well untilI am about to use the package for analysis:

2: using the .fa file for analysis

(base) [caiqi@midway2-login2 PUM2_CLIP]$ pureclip -i aligned.f.duplRm.pooled.R2.bam -bai aligned.f.duplRm.pooled.R2.bam.bai -g ref.GRCh38.fa -iv 'chr1;chr2;chr3;' -nt 10 -o PureCLIP.crosslink_sites.bed

Protein-RNA crosslink site detection 
===============

Created look-up table for values from -2000 to 0 with step size 0.00333333 (size: 600000).
Loading reference ... 
ERROR: Can't load reference sequence from file 'ref.GRCh38.fa': Unexpected character 'M' found.

Can anyone help me out for these 2 bugs?

Thanks a lot,

Cai

[Kai_Qi]

Let me answer the question myself after several trying:

I downloaded the hg38 files instead of GRCh38 and make it through. Does not know if the results are satisfying but this way can make the script go through.

Thanks,