User: SDin

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SDin0
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Posts by SDin

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Pysam.view report 'pysam.utils.SamtoolsError: "samtools returned with error 1: s
... I decide to use command line mode of samtools at last, thanks for your kind help. ...
written 4 days ago by SDin0
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Comment: C: Pysam.view report 'pysam.utils.SamtoolsError: "samtools returned with error 1: s
... Thanks for your kind help, it can run now. But when I run the code, there are some messy code on the screen: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\x00\xdbx:Z\xe0\x9d\x00\x00\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00BC\x02\x00\x1b\ ...
written 8 days ago by SDin0
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Comment: C: Pysam.view report 'pysam.utils.SamtoolsError: "samtools returned with error 1: s
... Hmmm, no, the 'samtools view' works. So it is quite weird.. ...
written 10 days ago by SDin0
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Comment: C: Pysam.view report 'pysam.utils.SamtoolsError: "samtools returned with error 1: s
... It is already in the command line.. ...
written 11 days ago by SDin0
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Pysam.view report 'pysam.utils.SamtoolsError: "samtools returned with error 1: stdout=, stderr=samtools view: invalid option -- ' ''
... Hi there, I am a beginner in this area. I am trying to use pysam for extract some reads. My code is pysam.view("-u -f 8 -F 260","/usr/local/virussite/input.bam","-o","output2.bam") and pysam.view("-u -f 8 -F 260","/usr/local/virussite/input.bam > output2.bam") both will report ...
samtools pysam written 11 days ago by SDin0 • updated 11 days ago by ATpoint14k
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Questions from beginner: Barcode of Single cell RNA-seq
... Hi there, I am a freshman in this area. When I reading the review of it, I am a little bit confused by the barcode of it. In the review, it said barcode is added by PCR. So it is on the end of the sequence. My question is: When we doing the NGS, the sequences will go through 'fragmentation' step ...
next-gen rna-seq sequencing written 11 days ago by SDin0
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Comment: C: extracting the soft clipped seq only from a sam file
... Hi, IrK, sorry for bothering you. Have you solved this problem? It will be very appreciated that you can give some advice. ...
written 27 days ago by SDin0
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Comment: C: Samtools: Question about filtering BAM file using flag
... I got it. Many thanks for your kind help! ...
written 4 weeks ago by SDin0
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Samtools: Question about filtering BAM file using flag
... Hi there, I am trying to filter BAM file with their 'flag' column. I am a little confuse about the meanings of, for example, samtools view -f 4 -F 264 ..... I check the documentation, and notice -f means 'what I want' and '4' means 'read unmapped' -F means 'wipe off' and '2 ...
next-gen alignment sequencing written 4 weeks ago by SDin0 • updated 4 weeks ago by Friederike3.3k

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