User: MAPK

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MAPK1.6k
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Posts by MAPK

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Comment: C: Extract SRA reads per RG using fasterq-dump
... I actually downloaded SRA with `prefetch` first and then used that in `fastq-dump` `-Z "./${SRR}"`. Not sure if this is the correct way to use downloaded SRA folder. ...
written 3 hours ago by MAPK1.6k
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Extract SRA reads per RG using fasterq-dump
... I am trying to download dbGAP SRA samples. I used to use fastq-dump with the following command below, but for this particular project fastq-dump is running really slow because of larger datasets. So, I wanted to use fasterq-dump tool, but couldn't figure out how I could split reads per RG tags. I tr ...
sra fasterq-dump dbgap written 4 hours ago by MAPK1.6k
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Answer: C: Suggestions on Labtop Mac for Bioinformatics
... I would buy Windows i7 laptops for less price. Recent Windows come with Windows Subsystem for Linux (WSL) or you can also install mobaxterm. ...
written 10 days ago by MAPK1.6k
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Comment: C: How to assign read groups to bam files?
... Thank you. So I don't need three different RGIDs for one sample/bam? Are you saying I can still merge 1000 samples in a joint call by having only one (unique) RGID per sample? I thought markduplicate step requires all read groups defined properly within each bam. ...
written 14 days ago by MAPK1.6k
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Comment: C: How to assign read groups to bam files?
... I have 1000 samples with same problem. Not 1000 bams for each sample. ...
written 14 days ago by MAPK1.6k
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Comment: C: How to assign read groups to bam files?
... Yes it is for just one sample as an example. ...
written 14 days ago by MAPK1.6k
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Comment: C: How to assign read groups to bam files?
... That's right. But how do I add three read groups to one bam? I am trying to use picard's AddOrReplaceReadGroups. ...
written 14 days ago by MAPK1.6k
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Comment: C: How to assign read groups to bam files?
... I think so, because these are unique. What I have right now is one RGID (Project name) for all 1000+ samples ...
written 14 days ago by MAPK1.6k
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Comment: C: How to assign read groups to bam files?
... Hi Pierre, I do have read information as shown in my question (I just updated). Is there a way I could use it? I can see these could be used as RGIDs. What else do I need to use and how do I do it? HS2000-1111A_136:4 HS2000-1111A_136:5 HS2000-1111A_136:5 ...
written 14 days ago by MAPK1.6k
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How to assign read groups to bam files?
... I have several BAM files. When we received these BAMs, they were assigned only one RGID. However, I was told that they actually have several read groups and were not correctly done. I checked the RGs: $samtools view -H 4029_PPNI_WGS.bam | grep "^@RG" @SQ SN:chr1 LN:249250621 @ ...
bam written 14 days ago by MAPK1.6k

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