User: luzglongoria
luzglongoria • 0
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Posts by luzglongoria
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... Thank you so much!. Your comment has been very helpful.
I just read that when I run
seqtk comp hg38.fa
I get :
chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts
I have been reading about what means each column :
**ts** transition ie. adacent A<=>G or C<=>T
...
written 1 day ago by
luzglongoria • 0
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... Hi everyone,
I have a .fasta file that I have created by running trinity (so it is an transcript assembly). I want to know the CG% for each contig and keep those with low % of CG. My data belong to a bird infected by Plasmodium and and only want contig with low CG% (because Plasmodium spp have low ...
written 1 day ago by
luzglongoria • 0
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... No. I downloaded the genome from NCBI. ...
written 1 day ago by
luzglongoria • 0
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... Hi,
I have done an assembly by using reads from a bird infected with a parasite (by using Trinity) >> Trinity.fasta
I have created a index for a genome by using:
gmap_build -d genome -k 15 GCF_000534875.1_SCA1_genomic.fa
A directory called "genome" has been create where now there is:
...
written 2 days ago by
luzglongoria • 0
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... Hi,
I have done a de novo transcriptome assembly, now I'm trying to map the assembled transcriptome to a genome of relative species. I have been reading about which program should I use. What do you think about using BBMap, Spaln or GMAP ? Which one fit better with this kind of analyses?
Thanks ...
written 3 days ago by
luzglongoria • 0
• updated
3 days ago by
Charles Warden ♦ 5.9k
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... Yes. I have been looking for this too but I only got answer for phyton but nothing for bash :( ...
written 8 weeks ago by
luzglongoria • 0
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... Thanks Pierre.
This command will calculate directly the CG content?
So, in my case, if my fastq file is called myfile.fastq the command will be:
> awk '(NR%4==2) {gsub(/[ATnNat]/,"");N+=length($0);}END{print N;}' myfile.fastq
Is it that correct?
...
written 8 weeks ago by
luzglongoria • 0
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... thanks! I had run FASTQC in my files before.
I just wanted to know a way of counting the % by using commands in bash :) ...
written 8 weeks ago by
luzglongoria • 0
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... Hi there,
I would like to know the CG content of some fastq file. I have this script:
This gives character count for all characters except As, Ts and Ns (and new lines):
cat file.fasta | grep -v ">" | tr -d aAtTnN"\n" | wc -c
24642235
This gives character count for all letters except ...
written 8 weeks ago by
luzglongoria • 0
• updated
8 weeks ago by
finswimmer ♦ 8.9k
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... hi,
I have two phylogenetic trees (extension .nex) and need to plot them face to face with links between them.
I have also done a .cvs file with the associations between these two trees.
However, when I try ro run the commands that I have found I got some error message:
> ### two trees
tree ...
written 9 weeks ago by
luzglongoria • 0
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