User: luzglongoria

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Posts by luzglongoria

<prev • 39 results • page 1 of 4 • next >
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Comment: C: How calculate CG content for each contig in an transcript assembly?
... 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 luzglongoria0
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How calculate CG content for each contig in an transcript assembly?
... 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 ...
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Comment: C: Mapping with GMAP: which output option shall I use?
... No. I downloaded the genome from NCBI. ...
written 1 day ago by luzglongoria0
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Mapping with GMAP: which output option shall I use?
... 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: ...
genome assembly transcriptome written 2 days ago by luzglongoria0
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Mapping transcripts to genome
... 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 ...
gene assembly rna-seq written 3 days ago by luzglongoria0 • updated 3 days ago by Charles Warden5.9k
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Comment: C: Calculate CG content in a fastq file
... Yes. I have been looking for this too but I only got answer for phyton but nothing for bash :( ...
written 8 weeks ago by luzglongoria0
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Comment: C: Calculate CG content in a fastq file
... 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 luzglongoria0
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Comment: C: Calculate CG content in a fastq file
... 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 luzglongoria0
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Calculate CG content in a fastq file
... 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 ...
rna-seq bash written 8 weeks ago by luzglongoria0 • updated 8 weeks ago by finswimmer8.9k
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Plots two phylogenetic trees face to face
... 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 ...
ape phytools trees written 9 weeks ago by luzglongoria0

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