User: omariqbal2017

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Posts by omariqbal2017

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How to check if a read in a Bam file is paired or not?
... From the flag bit 8, we can get obtain that the next segment in the template is unmapped so consequently, the read is not paired but this rule is not always true like in the case of flag value 129 so what's a reliable way to check if a read contains a pair or not? ...
reads paired reads bam sam single paired reads written 7 months ago by omariqbal20170
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Comment: C: How to convert from a cigar string to extended cigar string?
... 2 examples: - cigar string "100M" MD tag "43C5C43T6" output = "43=C5=C43=T6=". - cigar string "80M1I19M" MD tag "63T26C8" output = "63=T16=1+9=C9=" ...
written 7 months ago by omariqbal20170
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How to convert from a cigar string to extended cigar string?
... I have a cigar string and the MD tag of the corresponding read record and I want to get the extended cigar string. Is there any java/c/c++ code or library that allows me to do that? ...
extended cigar cigar c++ sam bam written 7 months ago by omariqbal20170 • updated 7 months ago by genomax59k
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What's the difference between half mapped reads and single paired reads?
... I'm new in the SAM file format and I need to know what are the main difference between a half mapped read and a single paired read, and if possible also need to know how to detect this differences in the flag of the read. ...
reads single reads bam sam paired reads written 8 months ago by omariqbal20170 • updated 8 months ago by d-cameron1.9k
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Comment: C: How to check if a read in a SAM file contains substitutions
... That's great, what exactly do I have to check in the NM tag? ...
written 8 months ago by omariqbal20170
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How to check if a read in a SAM file contains substitutions
... How I do check whether a read contains substitutions or not. I'm not sure if I should check the flag, the cigar or the sequence. ...
read bam sam c++ written 8 months ago by omariqbal20170 • updated 8 months ago by d-cameron1.9k
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Comment: C: Cannot open BAM files with the SeqAn library
... The output of file /home/omair/Programs/seqan/demos/tutorial/sam_and_bam_io/example.bam is /home/omair/Programs/seqan/demos/tutorial/sam_and_bam_io/example.bam: gzip compressed data, extra field and the output of find /home/omair/ -type f -name "example.bam" is /home/omair/Programs/seqan/ap ...
written 9 months ago by omariqbal20170
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Cannot open BAM files with the SeqAn library
... For some reason, I cannot open BAM files using the SeqAn library. While I try to open by executing the following code: CharString bamFileName = getAbsolutePath("demos/tutorial/sam_and_bam_io/example.bam"); I get the following error: ERROR: Could not open /home/omair/Programs/seqan/demos/tutorial/ ...
sequencing bam seqan c++ written 9 months ago by omariqbal20170

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