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Recent Replies
Comment: How to sort gff3 according to chromosome order?
by
BioinfoBee
•
0
using sort -k1,1 doesn't keep the order of child features of each gene in output.
Comment: How to sort gff3 according to chromosome order?
by
Ram
39k
You're sorting by chromosome AND co-ordinates. Try just `sort -k1,1`
Comment: How to sort gff3 according to chromosome order?
by
BioinfoBee
•
0
it does sort but not able to keep the child features (mRNA, CDS, exon) in proper order. For example, I can sort using: sort -k1,1 -k4,4n -k…
Comment: How to sort gff3 according to chromosome order?
by
Pierre Lindenbaum
154k
uh ? what about the [sort][1] command ?
[1]: https://man7.org/linux/man-pages/man1/sort.1.html
Comment: What does canonical transcript mean in the context of VEP
by
Ram
39k
> Does that mean the fully functional gene most folks think of when thinking of their favorite gene?
That ... doesn't make much sense. Did…
Answer: What does canonical transcript mean in the context of VEP
by
Pierre Lindenbaum
154k
https://www.ensembl.org/info/genome/genebuild/canonical.html
> The Ensembl Canonical transcript is a single, representative transcript ide…
Answer: Why is coordinate sort required before findng read depths?
by
Ram
39k
In an unsorted BAM file, reads can be in any random order. In a co-ordinate sorted BAM file, reads are in the order in which they map to th…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
▴
70
how does it correspond to 27.2 ? or these are the other proteins ?
Comment: Merge different vcf files
by
Ram
39k
Normalize them first using `vt normalize` or `bcftools norm` - they need to be in left-aligned parsimonious representation before you can d…
Answer: integrate single cell RNA sequencing data
by
John Ma
▴
300
You need to perform batch effect removal for these. Seurat has its integration protocol, and if you use scverse on Python, the usual choice…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
I added the link for NCBI "book" since DIAMOND seems to follow the format/reporting structure for blast+ results. While the numbers shown i…
Comment: bcftools "--filter-logic" flag, what + means?
by
Ram
39k
`PASS` + `filter_name` is `filter_name`, not `PASS,filter_name`. PASS means the locus hit no filter. You'll never see a `PASS,<something>`.…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
Alexander
▴
70
Thank you for the reply ! I got seems to be even more puzzled here - we see "identities" 95% while in the example "pident" is 27.2 - so …
Comment: bcftools "--filter-logic" flag, what + means?
by
Eugene A
▴
170
Thanks a lot for the explanation!
Comment: How GATK pipeline called a homozygeous alternate allele (1/1) although one copy
by
Ram
39k
> Do you mean that because it is 1/1, so both copies is different from the reference and that is why the 0 in the AD is because no reads is…
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