Hi,
I would need some help on to proceed for WES analysis.
I observed from different posts in the forum that the paired end reads can be aligned separately and the resulting SAM files are merged for further analysis. I would like to know on how to consider the data from different lanes while doing alignment.
Should i merge the data from different lanes for L{1,2}_R1.fq, L{1,2}_R2.fq into separate files or perform alignment for different read type(1,2) and different lanes specific data separately(4 times L1_R1.fq, L1_R2, L2_R1, L2_R2) and merge the SAM files for further analysis ?
Please advise.
Thanks
it's better to merge fastq and then perform alignment
You mean, merge data from different lanes L{1,2} of Read1.fq into a single file, L{1,2} of Read2.fq into another file right ?
Thanks
exactly
Hello deepue!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=51448
This is typically not recommended as it runs the risk of annoying people in both communities.
Thanks Pierre for your advise. I am trying to delete the other post and will take care of it from next time.
Could you please advise in this scenario ? Thank you !