West Slavic KRA-samples

[Lemminkäinen]

I am processing those aDna fastq files and it is somewhat boring. Maybe it takes a month? Anyone have done it? I have a dedicated power PC running it and I can keep it running what ever it takes, just asking.

[Peterski]

I am processing those aDna fastq files and it is somewhat boring. Maybe it takes a month? Anyone have done it? I have a dedicated power PC running it and I can keep it running what ever it takes, just asking.

What software are you using to process them? It must be very slow.

[Lemminkäinen]

What software are you using to process them? It must be very slow.

BWA.

[Peterski]

BWA.

Do you merge all FASTQ files together and then convert to BAM?

There are plenty of FASTQ files per every individual sample.

[Lemminkäinen]

Do you merge all FASTQ files together and then convert to BAM?

There are plenty of FASTQ files per every individual sample.

Yeah, this was the plan and I concatenated files before running BWA. Ihave never before had as big fastq files as these files. There are a lot short reads as you can expect for aDna files. I tried first using the mem parameter, but didn't like the disc traffic it made, because 32gb memory was eaten soon and BWA started to use swap and now use the sampe sequence. But hard to say without testing would be better, to let memory swapping and keep cpu low OR keeping used memory small (sampe) and let the cpu run high. Obviously created bam files will be even tens gigabytes