User: jing.mengrabbit

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Posts by jing.mengrabbit

<prev • 27 results • page 1 of 3 • next >
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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 7 weeks ago by jing.mengrabbit0
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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 7 weeks ago by jing.mengrabbit0
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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 7 weeks ago by jing.mengrabbit0 • updated 7 weeks ago by h.mon15k
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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 3 months ago by jing.mengrabbit0
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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 3 months ago by jing.mengrabbit0
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How to read two non-consecutive lines in a file once in python
... Hi, I want to read two non-consecutive lines once in a very big pileup file in python, that is, the expected result is the following(the number is the line number): 1 6 (the first time reads the 1st and 6th line) 2 7 (the second time reads the 2nd and 7th line) 3 8 (the third time reads the 3rd a ...
genome sequencing written 3 months ago by jing.mengrabbit0 • updated 3 months ago by mohammadhassanj30
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samtools pileup format: insertions and deletions' quality
... I have some questions about samtools pileup format http://samtools.sourceforge.net/pileup.shtml: 1. at the read base column, a symbol `^' marks the start of a read segment which is a contiguous subsequence on the read separated by `N/S/H' CIGAR operations. The ASCII of the character followin ...
genome alignment sequencing written 3 months ago by jing.mengrabbit0 • updated 3 months ago by John Marshall1.2k
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Comment: C: how to use the option of --rf and the options of -a and -a -a (-aa) in samtools
... Thanks for your time. The following is the reply from samtools developers about the difference between -a and -a -a (-aa): -a and -aa is all vs absolutely all (bad term I know). The difference is to do with references with zero coverage. For example if we have a file with @SQ headers for all chro ...
written 3 months ago by jing.mengrabbit0
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Comment: C: how to use the option of --rf and the options of -a and -a -a (-aa) in samtools
... Thanks for your time. The following is the reply from samtools developers about the difference between -a and -a -a (-aa): -a and -aa is all vs absolutely all (bad term I know). The difference is to do with references with zero coverage. For example if we have a file with @SQ headers for all chro ...
written 3 months ago by jing.mengrabbit0
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Comment: C: how to use the option of --rf and the options of -a and -a -a (-aa) in samtools
... Thanks Kevin for your answer. Do you know what is the difference between -a and -a -a (-aa)? ...
written 4 months ago by jing.mengrabbit0

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