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Recent Replies
Comment: Snakemake and STARsolo
by
Ram
33k
I stand corrected. I just noticed that OP is trying to run Snakemake without specifying a target.
Comment: How to extract translated sequence of a partcular gene by parsing GenBank file
by
cpad0112
15k
check if following code works out (be mindful of copying errors from web):
import sys
from Bio import SeqIO
gbinput= sys.argv[…
Answer: collapsing coordinate information from a blast result
by
Mensur Dlakic
★
11k
I think this program does almost exactly what you want.
https://sourceforge.net/projects/weinberg-overcluster2/
Comment: Snakemake and STARsolo
by
Jeremy Leipzig
20k
i think `SAMPLES ,= glob_wildcards` is valid but i do prefer to know what I am trying to make rather than let a directory run the show http…
Comment: Snakemake and STARsolo
by
Ram
33k
Follow Jeremy's advice. Your Snakefile is badly formed and the line outside the rule breaks everything.
Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
by
Dunois
▴
780
I'd add to @genomax 's point that if you're going to run a search against `NR` on a local machine, it's probably unwise at this point to us…
Comment: Bedtools intersect 0- and 1-based coordinate files
by
maxrwjones898
▴
10
Ah wonderful, good to know! Brilliant answer and thanks for the code / outputs to back it up.
Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
by
GenoMax
101k
> clients proprietary sequences which cannot by processed on public
> website.
No option but to download `nr` indexes and do the search lo…
Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'?
by
matt
▴
10
I would like to be able to do ‘blastp’ with clients proprietary sequences which cannot by processed on public website.
Until now I did it …
Answer: Bedtools intersect 0- and 1-based coordinate files
by
ATpoint
49k
> Does bedtools intersect automatically take this difference into account?
Yes, it is quite a smart one.
Example (BED vs GTF, random file…
Comment: Issue on downloading fastPHASE in Mac
by
4galaxy77
▴
510
Out of polite curiosity, what use to people have for fastPHASE in 2021? I believe it's still the most accurate method, but pretty slow. So …
Comment: Snakemake and STARsolo
by
Jeremy Leipzig
20k
one of them is `{sample}.Aligned.out.sam`. Start by creating a target variable that point to the sam files you want produced
SAMPLES =…
Comment: T-test analysis for gene expression comparison
by
bioinformatics2020
▴
580
THIS! You need to go back and learn about what type of distribution is used for a t-test. Then start understanding the distributions that g…
Comment: Warning messages: In svgStyleAttributes(style, svgdev) : Removing non-S
by
xxxxxxxx
▴
20
arrayQualityMetrics version- 3.47.0
Comment: Liftover vcf file from hs37d5 assembly to b37 assembly
by
Pierre Lindenbaum
135k
don't you just have to rename the chromosomes (if needed) and discard the chromosomes that are not present in the other reference ?
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