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1 vote

Problem while mapping reads to mtDNA (SortSam)

The first error seems to come from picard when sorting the sam file: SAMFormatException: SAM validation error: ERROR: Read name M02699:57:000000000-LG9CK:1:1119:16584:12259, CIGAR M operator maps off ...
Cloudberry's user avatar
0 votes

Convert BAM to properly paired FASTQ files

Not sure what is the reason you are realigning (older version of the genome? different mapper?) but probably you want to have read pairs even if only one in the pair was mapped to the region of ...
darked89's user avatar
  • 358
4 votes
Accepted

Different line length in sequence 'chrY'

The error message is accurate as the downloaded fasta file got corrupted. Printing all the contigs, using the command below (the quotes around > are important, ...
Wouter De Coster's user avatar
1 vote
Accepted

Pysam - fetch reads within region

Looking at the CIGAR alignment, there is a 167,903bp gap followed by a 266,888bp gap after the starting match point. That second gap spans the region that you have specified. ...
gringer's user avatar
  • 14.3k

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