User: jing.mengrabbit

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Posts by jing.mengrabbit

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Comment: C: no successful variants lifted over from hs37d5_plusRibo_plusOncoViruses_plusERCC
... Yes, they have different chromosome names. ...
written 4 weeks ago by jing.mengrabbit10
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no successful variants lifted over from hs37d5_plusRibo_plusOncoViruses_plusERCC.fa to GRCh38
... I ran picard LiftoverVcf to lift over a VCF file from hs37d5_plusRibo_plusOncoViruses_plusERCC.fa to GRCh38 with chain file hg19ToHg38.over.chain, but no successful variants are lifted over. The following is the output: INFO 2018-07-19 11:30:39 LiftoverVcf Loading up the target reference genome. ...
assembly written 4 weeks ago by jing.mengrabbit10
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inaccurate max per-file depth in samtools mpileup
... Hi, I run samtools mpileup and set the -d 100 (max per-file depth), and that is the ouput information: [mpileup] 1 samples in 2 input files Set max per-file depth to 8000 Why the output is different from What I set? ...
sequencing written 5 weeks ago by jing.mengrabbit10
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Comment: C: how to split a coordinate-sorted bam file by read group
... Thanks for your reply. It works now with your help! ...
written 5 weeks ago by jing.mengrabbit10
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how to split a coordinate-sorted bam file by read group
... Hi, I have a coordinate-sorted bam file, and its read group information in the header is: @RG ID:0 PL:ILLUMINA SM:COLO829_Normal_Tgen PU:H0CGCADXX:1:none @RG ID:1 PL:ILLUMINA SM:COLO829_Normal_Tgen PU:H0CGCADXX:2:none @RG ID:2 PL:ILLUMINA SM:COLO829_Normal_Tgen PU:H0CGCADXX:3:none @RG ID:3 PL:IL ...
sequencing written 5 weeks ago by jing.mengrabbit10 • updated 5 weeks ago by finswimmer4.4k
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Comment: C: samtools mpileup's options -b (more than one bam file) and -r cannot be used tog
... Thanks for your advice. ...
written 3 months ago by jing.mengrabbit10
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Comment: C: samtools mpileup's options -b (more than one bam file) and -r cannot be used tog
... Thanks for your reply. I misunderstood the helper documentation. It should be -l instead of -r as you said. ...
written 3 months ago by jing.mengrabbit10
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samtools mpileup's options -b (more than one bam file) and -r cannot be used together
... Hi, I would like to generate a mpileup file from 2 bam files in some regions instead of the whole chromosomes: samtools -b bam_list_file -r regions_to_be_parsed.bed > mpileup_from_two_bam_files.pileup The content in the bam_list_file is ~/1.bam ~/2.bam but an error was given: [E::mpileup ...
software error sequence written 3 months ago by jing.mengrabbit10 • updated 3 months ago by h.mon18k
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Comment: C: How to read two non-consecutive lines in a file once in python
... It works for a big file. Thanks for your help! ...
written 5 months ago by jing.mengrabbit10
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Comment: C: How to read two non-consecutive lines in a file once in python
... My pileup file is too big, so the program will be crashed. But thanks for your time! ...
written 5 months ago by jing.mengrabbit10

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