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jianhong / ATACseqQC

ATAC-seq Quality Control
https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html
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Error on running splitBam #32

Closed hchetia closed 3 years ago

hchetia commented 4 years ago

While running the command objs <- splitBam(bamfile, tags=tags, outPath=outPath, txs=txs, genome=genome, conservation=phastCons100way.UCSC.hg38) I get the following error- Error in asMethod(object) : cannot coerce a non-logical 'Rle' or a logical 'Rle' with NAs to an IRanges object

jianhong commented 4 years ago

Thank you for reporting this. Could you share a subset of your data for me to debug?

hchetia commented 4 years ago

Hi Jian, Pls let me know which file format would you like me to share?

jianhong commented 4 years ago

It will be great if you can share the mimimal size of bamfile which can repeat the error. Thank you.

hchetia commented 4 years ago

Please see attachment

sample.bam.zip

jianhong commented 4 years ago

Thank you for sharing. However, I can not index the file. It report error: is not a BAM file.

hchetia commented 4 years ago

Shall I share index and bam?

hchetia commented 4 years ago

Hi Jian, check out if this works.

Archive.zip

jianhong commented 4 years ago

Thank you. I will take a look soon.

Best!

Your sincerely,

Jianhong Ou

On Oct 7, 2020, at 3:17 PM, hchetia notifications@github.com wrote:

 Hi Jian, check out if this works.

Archive.zip

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

jianhong commented 4 years ago

I found the bug. It is caused by not enough nucleosome free reads for training. So please try without conservation score.

hchetia commented 4 years ago

Hi Jian, DO you think the bug you found was actually because I shared only a snippet of my whole dataset?

Meanwhile, I will try without conservation score.

jianhong commented 4 years ago

I don't think it is caused by a small bam file. Just try without conservation score.

On Fri, Oct 16, 2020 at 9:04 PM hchetia notifications@github.com wrote:

Hi Jian, DO you think the bug you found was actually because I shared only a snippet of my whole dataset?

Meanwhile, I will try without conservation score.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jianhong/ATACseqQC/issues/32#issuecomment-710715946, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABLBEAYTQWAKEJLSZYWG353SLDUQVANCNFSM4RRIV6SA .

-- Yours sincerely, Jianhong Ou

hchetia commented 4 years ago

Hi Jian, How many nucleosome free reads are typically required for generating a conservations score?

jianhong commented 4 years ago

typically it should be more than 15% of your total reads.