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mbasam
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@mbasam-21086
Last seen 5.1 years ago
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?
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.
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?
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?
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
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
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.
Thank you for your valuable insight. The test worked. Best regards!