I have one pair end sample with 3 Different Lanes.
Lane 1:- V300110856_L01_A01_1.fq.gz V300110856_L01_A01_2.fq.gz
Lane 2:- V300110856_L01_A02_1.fq.gz V300110856_L01_A02_2.fq.gz
Lane 3:- V300110856_L01_A03_1.fq.gz V300110856_L01_A03_2.fq.gz
So should I merge the lane data or Can i go ahead analyzing data from one Lane? They are prepared from same library.
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written
by
Nikhil •
1 answer
map each pair or read in parallel, set the read-group according to the lane ( https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups eg. PU ).
then merge the 3 bams.
yes if you need to process the data per sample (eg VCF calling)
less depth, less quality
Hi! Pierre, I am having the same query regarding merging reads of multiple lanes together. However, I am not being able to find any documented sources till date, neither any of the literature tell about whether to merge the reads or perform the downstream to individual PE reads from individual lanes. Can you please help me with the documentation, if available?
Thank you.
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Hi,
You should merge the 3 lanes by orientation, i.e., forward and reverse, and use the merged/combined files for analysis.
In bash you can merge the files by doing:
I hope this helps,
António