Question: ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
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gravatar for mbasam
12 weeks ago by
mbasam0
mbasam0 wrote:

All other parts of the ATACseqQC package works, but when the shiftGAlignmentsList command is ran to shift the reads and split the BAM files, the command fails with the following error: (all(elementNROWS)>3) is not TRUE. However, in R, when I run that line, it returns as TRUE. What is the exact error the script is running into? Is it a possible bug?

ADD COMMENTlink written 12 weeks ago by mbasam0

That step is checking whether or not all the paired reads are two reads (left and right). elementNROWS>3 means there are some of the pairs contain three or more reads in one pair.

Just in case there are anything unexpected, could you please share me your reads filtering codes and a small piece of bam which can repeat your error?

Jianhong.

ADD REPLYlink written 12 weeks ago by Ou, Jianhong1.1k

Hi Jianhong,

How can I send you these files and code? Can please provide me with an email address so that I could send you a link to the file and code?

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by mbasam0

My email address is listed in webpage: https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html

From: "mbasam [bioc]" noreply@bioconductor.org Reply-To: "reply+d1af6dba+code@bioconductor.org" <reply+d1af6dba+code@bioconductor.org> Date: Friday, June 21, 2019 at 2:16 PM To: "Jianhong Ou, Ph.D." jianhong.ou@duke.edu Subject: [bioc] C: ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error

Activity on a post you are following on support.bioconductor.orghttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=A5t6SSn5sKT8ePlSzwYVxxY1qNb50E30y2vsWCrNKPU&s=cVjXudh0KdiQgJmR37oK4TsEOBl_qaP2iNwqOMoNv2k&e=

User mbasamhttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_u_21086_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=A5t6SSn5sKT8ePlSzwYVxxY1qNb50E30y2vsWCrNKPU&s=I19USzS-G0Wu_y75stYgsJvVXaY17ivABk8iTcxLwKc&e= wrote Comment: ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE errorhttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_122128_-23122169&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=A5t6SSn5sKT8ePlSzwYVxxY1qNb50E30y2vsWCrNKPU&s=yelyeYj2kHAexouyJumXcUsAMeRphjVtDDyEmKL_KEQ&e=:

Hi Jianhong,

How can I send you these files and code?

ADD REPLYlink written 12 weeks ago by Ou, Jianhong1.1k

Hi Jianhong,

Here is the filter code: http://s3.amazonaws.com/mudaser/bamfiles/ATACseq_heatmap.R And here is subset of the bam file: http://s3.amazonaws.com/mudaser/bamfiles/chr21-filt.bam

ADD REPLYlink written 12 weeks ago by mbasam0

Hi Jianhong,

Here is the filter code: http://s3.amazonaws.com/mudaser/bamfiles/ATACseq_heatmap.R And here is subset of the bam file: http://s3.amazonaws.com/mudaser/bamfiles/chr21-filt.bam

ADD REPLYlink written 12 weeks ago by mbasam0

Hi,

Thank you for sharing your bam file with me. Please have a try to change the line

gal <- readBamFile(bamfile, tag=tags, asMates=TRUE, bigFile=TRUE)

to

gal <- readBamFile(bamfile, tag=tags, asMates=TRUE, bigFile=TRUE, flag = scanBamFlag(isSecondaryAlignment = FALSE, isUnmappedQuery = FALSE, isNotPassingQualityControls = FALSE, isSupplementaryAlignment = FALSE))

Because current ATACseqQC can not handle supplementary alignments.

Jianhong.

ADD REPLYlink written 10 weeks ago by Ou, Jianhong1.1k

Thank you for your valuable insight. The test worked. Best regards!

ADD REPLYlink written 10 weeks ago by mbasam0
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