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Reads are the sequences output by a sequencing machine after the raw signal (e.g. light, electricity) is converted into bases by a basecaller.

2
votes
A complete solution to validate a SAM/BAM file would be picard's ValidateSamFile. This will find many other issues with BAM files. http://broadinstitute.github.io/picard/command-line-overview.html#V …
answered Oct 2 '17 by Bioathlete
2
votes
Can you modify that to split up the reads into separate files or encode the cell barcode in the read description instead of the read name? …
answered Oct 17 '18 by Bioathlete
9
votes
It is still slow but grep has a -f option to take in a file samtools view inbam.bam | grep -f read_names.txt > read_locs.txt
answered Dec 6 '18 by Bioathlete
1
vote
Both of those depend on the application of the library. For example whole genome assembly of a mammal would require a larger library size than targeted re-sequencing of a virus. Also insert size var …
answered Nov 21 '17 by Bioathlete
4
votes
Typically I use samtools for operations like this. Specifically I use samtools view with either -r or -R flag depending on the use case. -r STR Output alignments in read group STR [null]. Note tha …
answered Oct 12 '19 by Bioathlete