Closed Hdang1234 closed 4 years ago
jianhong
commented
4 years ago The shiftGAlignmentsList is designed for proper mapped paired end reads. I suppose that there is mpos in the metadata. This is the reason. Do you set asMates=TRUE for readBamFile?
Hdang1234
commented
4 years ago Yes, I did. I wonder if it’s the samtools fixmate function that causes this problem. Thanks for getting back so fast.
jianhong
commented
4 years ago Do you mind to share me the files and scripts to repeat the error? I can fix the issue in my side.
Best!
Your sincerely,
Jianhong Ou
On Feb 26, 2020, at 9:12 AM, Hdang1234 notifications@github.com wrote:
Yes, I did. I wonder if it’s the samtools fixmate function that causes this problem. Thanks for getting back so fast.
From: JIANHONG OU notifications@github.com Sent: 26 February, 2020 08:42 AM To: jianhong/ATACseqQC ATACseqQC@noreply.github.com Cc: Hien Dang Hien.Dang@jefferson.edu; Author author@noreply.github.com Subject: Re: [jianhong/ATACseqQC] shiftGAlignmentsList after samtools fixmate error (#22)
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The shiftGAlignmentsList is designed for proper mapped paired end reads. I suppose that there is mpos in the metadata. This is the reason. Do you set asMates=TRUE for readBamFile?
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Hdang1234
commented
4 years ago Not sure how to share the big bam files, suggestions?
jianhong
commented
4 years ago Could you try to subset the bam file to a small one and share it to by CyVerse, see documentation at https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting Thank you.
On Wed, Feb 26, 2020 at 10:44 AM Hdang1234 notifications@github.com wrote:
sorting the BAM file.docx https://github.com/jianhong/ATACseqQC/files/4256686/sorting.the.BAM.file.docx
Not sure how to share the big bam files, suggestions?
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Hdang1234
commented
4 years ago Hi Jianhong,
I have shared the data with you. Thanks for your help.
jianhong
commented
4 years ago I can not locate the shared file. Could you share it again?
Jianhong.
On Mon, Mar 2, 2020 at 2:16 PM Hdang1234 notifications@github.com wrote:
Hi Jianhong,
I have shared the data with you. Thanks for your help.
From: JIANHONG OU notifications@github.com Sent: 26 February, 2020 11:05 AM To: jianhong/ATACseqQC ATACseqQC@noreply.github.com Cc: Hien Dang Hien.Dang@jefferson.edu; Author author@noreply.github.com
Subject: Re: [jianhong/ATACseqQC] shiftGAlignmentsList after samtools fixmate error (#22)
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Could you try to subset the bam file to a small one and share it to by CyVerse, see documentation at https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html#Hosting Thank you.
On Wed, Feb 26, 2020 at 10:44 AM Hdang1234 <notifications@github.com mailto:notifications@github.com> wrote:
sorting the BAM file.docx < https://github.com/jianhong/ATACseqQC/files/4256686/sorting.the.BAM.file.docx>
Not sure how to share the big bam files, suggestions?
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Hdang1234
commented
4 years ago I have shared it. Thanks
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jianhong
commented
4 years ago Thank you. I see the files. will keep you updated.
Jianhong.
On Thu, Mar 5, 2020 at 7:03 PM Hdang1234 notifications@github.com wrote:
I have shared it. Thanks
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jianhong
commented
4 years ago Hi Dang,
I got the problem. The issue is your bam file only contain reads in chr22. But you are checking the quality for chr1 and chr2. So there is no reads can be read into the function. Please try to change:
which <- gr[seqnames(gr) %in% c("chr1", "chr2")]
To: which <- gr[seqnames(gr) %in% c("22")]
I am updating the package to show an clear error when this happens.
Good Luck.
Jianhong.
On Fri, Mar 6, 2020 at 11:16 AM jianhong ou jianhong.ou@gmail.com wrote:
Thank you. I see the files. will keep you updated.
Jianhong.
On Thu, Mar 5, 2020 at 7:03 PM Hdang1234 notifications@github.com wrote:
I have shared it. Thanks
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Hdang1234
commented
4 years ago Oh - I ran the whole bam file before and got the same issue.
Sent from my iPhone
On Mar 6, 2020, at 11:49 AM, JIANHONG OU notifications@github.com wrote:
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Hi Dang,
I got the problem. The issue is your bam file only contain reads in chr22. But you are checking the quality for chr1 and chr2. So there is no reads can be read into the function. Please try to change:
which <- gr[seqnames(gr) %in% c("chr1", "chr2")]
To: which <- gr[seqnames(gr) %in% c("22")]
I am updating the package to show an clear error when this happens.
Good Luck.
Jianhong.
On Fri, Mar 6, 2020 at 11:16 AM jianhong ou jianhong.ou@gmail.com wrote:
Thank you. I see the files. will keep you updated.
Jianhong.
On Thu, Mar 5, 2020 at 7:03 PM Hdang1234 notifications@github.com wrote:
I have shared it. Thanks
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jianhong
commented
4 years ago Just try the new code for chr22 and let me know if there are any issues.
On Fri, Mar 6, 2020 at 11:57 AM Hdang1234 notifications@github.com wrote:
Oh - I ran the whole bam file before and got the same issue.
Sent from my iPhone
On Mar 6, 2020, at 11:49 AM, JIANHONG OU notifications@github.com wrote:
WARNING: External Email - This email originated outside of Jefferson. DO NOT CLICK links or attachments unless you recognize the sender and are expecting the email.
Hi Dang,
I got the problem. The issue is your bam file only contain reads in chr22. But you are checking the quality for chr1 and chr2. So there is no reads can be read into the function. Please try to change:
which <- gr[seqnames(gr) %in% c("chr1", "chr2")]
To: which <- gr[seqnames(gr) %in% c("22")]
I am updating the package to show an clear error when this happens.
Good Luck.
Jianhong.
On Fri, Mar 6, 2020 at 11:16 AM jianhong ou jianhong.ou@gmail.com wrote:
Thank you. I see the files. will keep you updated.
Jianhong.
On Thu, Mar 5, 2020 at 7:03 PM Hdang1234 notifications@github.com wrote:
I have shared it. Thanks
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jianhong
commented
4 years ago another possible issue is that your seqname style is ensembl but not UCSC. please try to change chr1, chr2 to "1", "2".
On Fri, Mar 6, 2020 at 11:58 AM jianhong ou jianhong.ou@gmail.com wrote:
Just try the new code for chr22 and let me know if there are any issues.
On Fri, Mar 6, 2020 at 11:57 AM Hdang1234 notifications@github.com wrote:
Oh - I ran the whole bam file before and got the same issue.
Sent from my iPhone
On Mar 6, 2020, at 11:49 AM, JIANHONG OU notifications@github.com wrote:
WARNING: External Email - This email originated outside of Jefferson. DO NOT CLICK links or attachments unless you recognize the sender and are expecting the email.
Hi Dang,
I got the problem. The issue is your bam file only contain reads in chr22. But you are checking the quality for chr1 and chr2. So there is no reads can be read into the function. Please try to change:
which <- gr[seqnames(gr) %in% c("chr1", "chr2")]
To: which <- gr[seqnames(gr) %in% c("22")]
I am updating the package to show an clear error when this happens.
Good Luck.
Jianhong.
On Fri, Mar 6, 2020 at 11:16 AM jianhong ou jianhong.ou@gmail.com wrote:
Thank you. I see the files. will keep you updated.
Jianhong.
On Thu, Mar 5, 2020 at 7:03 PM Hdang1234 notifications@github.com wrote:
I have shared it. Thanks
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-- Yours sincerely, Jianhong Ou
Hdang1234
commented
4 years ago The naming of the chrm was the reason it didn’t work. I just realigned it so it matches UCSC. Thanks for your help.
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Hello-
I used samtools (see below) to sort some bam files (paired end reads) and ran ATACseqQC code and ran shiftGAlignmentsList and got an error (see below):
The sort according to name
samtools sort -n sorted-chrM.bam -o nchrM.bam
Add ms and MC tags for markdup to use later
samtools fixmate -rm nChrM.bam -o fixmate.bam
Markdup needs position order
samtools sort -o fixmate.bam fixmatePos.bam
Finally mark duplicates
samtools markdup -r fixmatePos.bam sorted-chrM-markup.bam samtools index -@ 1 sorted-chrM-markup.bam
This error comes on:
Only single end reads Error in names(this.mpos) <- paste(mcols(attempt to set an attribute on NULL))
Any chance you can tell me if the fixmate is causing this error?