Question: Running 3 FASTQ files for WGBS
0
gravatar for Batu
19 months ago by
Batu170
Batu170 wrote:

I want to run some FASTQ files for WGBS, but there are 3 files for each sample as here. These are SRRxxx, SRRxxx_1 and SRRxxx_2 files. 1 and 2 are supposed to be paired-end files (~25GB each), but ENA shows the library layout as single (I've seen some other paired-end-looking samples have single library layout in ENA, it's probably a mistake). And the other file has much lower size than the others (~2GB), and I couldn't figure out where this single smaller file should be used. Glad if you help. Thanks...

wgbs methylation fastq • 344 views
ADD COMMENTlink written 19 months ago by Batu170
1
gravatar for ATpoint
19 months ago by
ATpoint40k
Germany
ATpoint40k wrote:

This seems to be a case where (for a reason I do not know) there is a paired-end component of the run (which is the majority of reads) and a single-end component. This is rare but I've definitely seen it before. I would use fastqc on all files separately to see if something is odd on any of them. If not, align the paired-end files as paired and the single-end one as single-end and then merge the BAM files. If this causes downstream problems with the tools you intend to use for analysis, simply discard the single-end file. It probably doesn't add much coverage anyway.

ADD COMMENTlink written 19 months ago by ATpoint40k

Thank you very much...

ADD REPLYlink written 19 months ago by Batu170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1433 users visited in the last hour