The error that I am receiving is:
[bwa_sai2sam_pe_core] paired reads have different names: "SRR567550.1.1", "SRR567550.1.2"
I think that the problem is the '.1' and '.2' and have attempted to resolve this using repair.sh from BBmap, as in bwa sampe: paired ends with different names. Unfortunately my fastq files are both ~8 GB and java runs out of memory even when allocating the maximum memory that I can and setting compression to 9 (max).
One idea that I have had is to just take the first column using awk, but this will result in information loss.
I am unsure how to resolve this. Is there a quick/efficient way to strip the '.1' and '.2' while preserving information?
1 answer
Download the original fastq format files for this sample from EBI-ENA here and avoid this issue altogether.
If you used fastq-dump to dump the reads out then you should have used -F option to get the original read headers without this extra stuff from SRA.
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