Vamsi Kodali

splice sites in junc-bed file to override default settings

2

I think the information in the junc-bed file can be better utilized by minimap2 in dealing with cases that deviate from the default settings. Two such cases: 1. When there...

Query length in SAM output

4

I would like to reconstruct the alignment directly from the SAM output produced by `diamond blastp`. To determine the length of the unaligned region on the C-terminus of the query,...

I am trying to compute genome coverage starting from a bam file. By default `bedtools genomecov` computes coverage for the entire genome. Is there a way to restrict this to...

Chimeric alignments spanning multiple adjacent genes

3

When aligning proteins with paralogs located in a cluster, `miniprot` produces alignments encompassing two or more distinct genes. For example, aligning mouse protein NP_001036176.1 to human chromosome 1 (NC_000001.11) returns...

Negative length for introns in cs:Z: tag

4

I noticed this when testing for #33. In the example shown below, the `cs:Z:` tag uses the following to represent an intron: `~gt-1ag`. Is this expected? ```bash $ efetch -db...

From what I can tell, `fastp` expects the input files to be in FASTQ format. Lately, SRA has stopped including original base qualities in the FASTQ files (all qualities are...