shiftGAlignmentsList time

[josruirod]

Hi, congrats on the package. I'm going to integrate it in my pipelines
I am particularly interested on shiftGAlignmentsList. I think it's really useful to shift reads while keeping bam format, even paired end. This is interesting for downstream analysis purposes.
However, the importing bam file+shifting + exporting is taking a lot of time for averaged size bam files.

Just wanted to ask if there is any chance that this gets improved, maybe giving the option to use more threads? Don't know if it's possible.

Thank you,

[JIANHONG OU]

Hi, Thank you for the comments. The memory and time cost is a big issue of ATACseqQC. Now I don’t have good solution for that. One Possible solution may split the bam file into several sub files and run it in multiple threads. Otherwise we need rewriting the code by c. Best! Your sincerely, Jianhong Ou

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On Jun 9, 2018, at 6:46 AM, josruirod ***@***.***> wrote: Hi, congrats on the package. I'm going to integrate it in my pipelines I am particularly interested on shiftGAlignmentsList. I think it's really useful to shift reads while keeping bam format, even paired end. This is interesting for downstream analysis purposes. However, the importing bam file+shifting + exporting is taking a lot of time for averaged size bam files. Just wanted to ask if there is any chance that this gets improved, maybe giving the option to use more threads? Don't know if it's possible. Thank you, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[josruirod]

Sounds good, I hope this in your to do list.

Thank you for your insights

[JIANHONG OU]

Hi josruirod,

I improved the shiftGAlignmentsList function in the development version. Please have a try. Thank you.

[josruirod]

Thank you, appreciate the heads ups. I think the bigFile argument in readBamFile helps as well