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Popular Question to
predeus
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1.8k
Scholar to
rpolicastro
8.8k
Popular Question to
ieie
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Scholar to
chrchang523
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Recent Replies
Comment: Deleting all the rows from ANY column that contain a key word
by
brunobsouzaa
▴
720
`sed` can also do the job for you
sed '/Eukaryota/d' your_in_file > your_out_file
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
Bioinfo
•
0
@rpolicastro yes they do have the h5ad data but I cannot figure how to make a use out of it. It seems they just cluster things and that is …
Comment: pymol for superimpose by python script
by
iamsmor
•
0
Thank you so much, you really wonderful person, spend your time for long detailed explaination.
Answer: Problem using FastML for ancestral sequence reconstruction
by
Mensur Dlakic
★
19k
It does not seem that you understand the meaning of this error message:
> sh: 1: cannot create outdir/fastml.std: Directory nonexistent
…
Comment: aligner for CORRECTED pacbio long reads
by
gconcepcion
▴
280
This is a very old and outdated link, what is it exactly that you are trying to do?
Align PacBio HiFi reads to a reference?
Try minimap…
Comment: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
by
sunnykevin97
▴
760
You have to use the nucleotide (CDS) alignment file as input.
Comment: What Is Ad (Allelic Depth) In 1000Genomes Vcf?
by
Maryam
•
0
Hello,
This post is so helpful.
My question is according to quality scoring of variants, the good AD threshold should be >8. Then how…
Comment: Incomplete alignment EMBOSS needleall
by
lieven.sterck
14k
not sure if it takes fastq as input (though yes, there example on their site is named .fastq , but when you look at that file it is a fasta…
Comment: Extract sequence from Fasta using header
by
GenoMax
117k
@princy: You have asked many questions on biostars over the last few months but appear not to have validated any of them. Accepting answers…
Answer: Extract sequence from Fasta using header
by
lieven.sterck
14k
`seqkit` will be able to do this. (subprogram `seq` )
(alternative, if you have a blastdb of that fasta file, you can also get them by u…
Answer: Extract sequence from Fasta using header
by
GenoMax
117k
See: https://www.biostars.org/p/434016/#434038
Comment: Best pipeline for RNAseq assembly and analysis (or help with stringtie assembly)
by
Katherine
•
0
I thought that the file I used was the most up to date. Here is the header of the file:
gff-version 3
!gff-spec-version 1.21
!processor…
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
rpolicastro
8.8k
They provide an h5ad file, which may contain the already processed data, plus associated cell and feature metadata. If so, you should load …
Answer: Extract header from fasta file
by
cpad0112
20k
$ awk -F "_|:" -v OFS="_" '/^>/{print ">"$2,$3,$4,$5,$6};!/>/' test.fa
>TRINITY_DN74698_c0_g1_i1
MRIRSVVFTLRPRAKWMAPSSGMRL…
Answer: analyzing a single cell and searching for a specific gene using single cell data
by
jared.andrews07
★
13k
I'd recommend you read what goes into a single cell analysis. The [Orchestrating Single Cell Analysis](http://bioconductor.org/books/releas…
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