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Old 03-31-2015, 12:46 AM   #1
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Location: Europe

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Default BWA alignment using paired end reads from different lanes


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.

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Old 03-31-2015, 01:40 AM   #2
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cross posted:
lindenb is offline   Reply With Quote

bwa, lane, paired end reads

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