Comments (4)
Is this related to #6, and specifically, are you interested in read counts (counting the number of reads mapped) in both issues rather than nucleotide coverage?
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Is this related to #6, and specifically, are you interested in read counts (counting the number of reads mapped) in both issues rather than nucleotide coverage?
Hi telatin,
these are two independent issues. Both of them are preferred with read counts (per base is covered by how many reads). For example, if 3,000,000 reads were sequenced in total, chr1:123-123 covered by 3,00 reads, the RPM for this base will be 100.
Best,
Keren
from bamtocov.
Ok, consider that bamtocov
computes nucleotide coverage, while bamtocounts
focuses on read counts on a target, and it has some options for normalization already built-in.
from bamtocov.
Ok, consider that
bamtocov
computes nucleotide coverage, whilebamtocounts
focuses on read counts on a target, and it has some options for normalization already built-in.
Oh, I must misunderstand the read counts and nucleotide coverage. Both of these #6 and #7 are preferred with nucleotide coverage.
See the same example above, if 3,000,000 reads were sequenced in total, chr1:123-123 covered by 300 reads, then the nucleotide coverage and RPM for this base (chr1:123-123) will be 300 and 100.
Best,
from bamtocov.
Related Issues (12)
- [BUG] Avoid allowing --report when not target is supplied HOT 1
- "invalid integer: everything" when trying to run BamToCov HOT 3
- `bamtocov` generated "ERROR: coverage went backwards from 0 to 0"
- [BUG] run time exceeds > 6 hours human exome HOT 1
- [BUG] Multiple bams and no regions produce inconsistent behaviour HOT 1
- Multibam processing using multiple threads
- Multiple BAMs and no target can count chromosomes instead
- Missing information of strand function HOT 2
- add an argument for bamtocov to allow the extension of reads to fragment size from single-end sequencing data HOT 4
- A way to calculate coverage breadth HOT 2
- How did bamtocov deal with paired-end bam from stranded libraries? HOT 1
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