User: luzglongoria

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luzglongoria20
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Posts by luzglongoria

<prev • 52 results • page 2 of 6 • next >
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Comment: C: Basic question about SWISSPROT
... Thank you so much Bastien. I have run the previos command: TransDecoder.LongOrfs -t Trinity.fasta and TransDecoder.Predict -t Trinity.fas So then I have files: Trinity.fasta.transdecoder.bed Trinity.fasta.transdecoder.cds Trinity.fasta.transdecoder.pep Can I use as a data ...
written 5 weeks ago by luzglongoria20
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Basic question about SWISSPROT
... Hi there, I have been working on my transcriptome assembly and now it is time to start doing functional annotation. I have read that a way to do it is using SWISSPROT. The command that I have found is something like: blastx -db ~/shared_ro/dbs/sprot.mini.pep -query Trinity.fasta -num_thr ...
swissprot rna-seq transcriptome written 5 weeks ago by luzglongoria20
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How to delete some contigs in an assembly
... Hi there, I'm new in bioinformatics tools and I need help. I tell you what I have done :) I have an assembly from Trinity and I wanted to know the CG content of each assembly so I generated a file with this information and I imported to R. Then, I calculated the CG content of all my contigs in ...
assembly rna-seq R written 7 weeks ago by luzglongoria20 • updated 7 weeks ago by genomax64k
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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 9 weeks ago by luzglongoria20
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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 ...
cg content assembly contig rna-seq transcriptome written 9 weeks ago by luzglongoria20 • updated 8 weeks ago by bioExplorer3.7k
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Comment: C: Mapping with GMAP: which output option shall I use?
... No. I downloaded the genome from NCBI. ...
written 9 weeks ago by luzglongoria20
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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 9 weeks ago by luzglongoria20
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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 9 weeks ago by luzglongoria20 • updated 9 weeks ago by Charles Warden6.5k
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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 4 months ago by luzglongoria20
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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 4 months ago by luzglongoria20

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