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Recent Replies
Comment: How to split a long protein sequence in small sequences with same header?
by
cpad0112
21k
if fasta file is as simple as that, you can try following simple code:
$ bioawk -c fastx '{print ">"$name; print substr($seq,1,length(…
Comment: Supplementary alignments in BAM-file
by
GenoMax
117k
Does this address
> i want the whole read to be filtered out whenever it contains
> supplementary alignments from the bamfile and not on…
Answer: Supplementary alignments in BAM-file
by
Pierre Lindenbaum
146k
add `-e '![SA]'` to your samtools view command ( http://www.htslib.org/doc/samtools.html#FILTER_EXPRESSIONS )
Comment: Minimum and maximum depth filert - vcftools
by
Pierre Lindenbaum
146k
vcftools is deprecated use `bcftools -i 'INFODP>1 && INFO/DP<1000'`
Comment: Filtered reads from assembly and raw reads?
by
GenoMax
117k
> can be used to get reads from a de-novo assembly if I have the raw
> reads?
If you have an assembly then the individual reads are no lon…
Answer: ESTIMATION OF LEVEL OF CYTOKINES FROM BULK RNAseq
by
Rafael Soler
▴
430
Hello Leticia,
I don't know much about Cybersort analysis, but you can check genes related to `cytokine activity` GO Term http://www.inf…
Comment: Supplementary alignments in BAM-file
by
mokbel73
•
0
![enter image description here][1]
[1]: /media/images/d8927d0a-865b-44d3-82de-b277c7b6
Comment: resolving specific clusters from data (spectral clustering)
by
benformatics
★
2.9k
I like your suggestions, I will try that. It's gene coverage at specific coordinates.
Comment: enhanced volcano label point
by
cpad0112
21k
How about this?:
ggplot(data=dat, aes(x=x, y=y, color=label)) +
geom_point(size=10)+
geom_point(data=dat[dat$label=="B",]…
Comment: resolving specific clusters from data (spectral clustering)
by
ATpoint
62k
What is x and y? What kind of data is that? Did you try a graph-based clustering based on these two dimensions? So building a KNN/SNN graph…
Comment: How to split a long protein sequence in small sequences with same header?
by
GenoMax
117k
Tagging: https://www.biostars.org/u/4664/
https://www.biostars.org/u/4664/ : It appears that `seqkit` is not working for this task. Can yo…
Comment: How to split a long protein sequence in small sequences with same header?
by
FelipeMSD
•
0
Thank you very much JC! Just used that and it worked very well :)
Answer: The nightmare of coordinate systems
by
tomas4482
▴
170
https://tidyomics.com/blog/2018/12/09/2018-12-09-the-devil-0-and-1-coordinate-system-in-genomics/
https://genome-blog.soe.ucsc.edu/blog/20…
Answer: How to split a long protein sequence in small sequences with same header?
by
JC
13k
Perl code:
#!/usr/bin/perl
use strict;
use warnings;
my $word_size = 6;
$/="\n>"; # read sequ…
Comment: How to split a long protein sequence in small sequences with same header?
by
FelipeMSD
•
0
To be honest, Joe, I also tried **seqkit split2 -l** in the past and, just as Hugo was saying, by using this we do not get the result we wa…
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