User: cl

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cl0
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Posts by cl

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Comment: C: Read name not stored in CRAM file. Is it possible to create new read names for r
... That would of course be a possibility, but then each read would become a single-end read, and I would of course like to retain the paired-end read (i.e. one uniqe read name for a pair of reads). I wonder if it is possible to match paired reads from the other information in the alignment section of t ...
written 18 days ago by cl0
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Comment: C: Read name not stored in CRAM file. Is it possible to create new read names for r
... New names have been automatically generated during decoding, but the names are identical for many reads. To give one example: After converting a 5 mb region from a CRAM file into a BAM file, I have 2,797,216 reads in the BAM file. However, in this BAM file, I only have 177,983 unique read names. Mo ...
written 18 days ago by cl0
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Read name not stored in CRAM file. Is it possible to create new read names for remapping?
... I have received some CRAM files with paired-end WGS data. I would like to remap the reads in a specific region to another reference. However, most of the template/read names have the format `filename.cram:21937611`, so I suspect that the CRAM files have been stored with `samtools ... lossy_names=1` ...
cram bam samtools sequencing written 18 days ago by cl0 • updated 14 days ago by jkbonfield440

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