User: marcelolaia

gravatar for marcelolaia
marcelolaia10
Reputation:
10
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New User
Location:
Brazil
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Google Scholar Page
Last seen:
8 months, 3 weeks ago
Joined:
8 years, 4 months ago
Email:
m**********@gmail.com

I am a Forest Engineer working with genomics, transcriptomics and proteomics. I love Bioinformatics, but don't have good skills on programming.

Posts by marcelolaia

<prev • 19 results • page 1 of 2 • next >
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sh: 1: /usr/bin/hisat2_read_statistics.py: not found - Warning or Error?
... Hi, I run the hisat2 like this: $ for f in `ls ./raw_data/*.fq.gz | sed 's/_[12].fq.gz//g' | sort -u`; do hisat2 -p 1 -x ./HiSat2/GCA_000389695.3_Cfim3.0_genomic_hisat2 -1 ${f}_1.fq.gz -2 ${f}_2.fq.gz -S ${f}.sam; done $ and got this message: sh: 1: /usr/bin/hisat2_read_statistics.py: ...
hisat alignment rna-seq hisat2 written 8 months ago by marcelolaia10
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Answer: A: Extract fasta sequences based on ids file
... I solved it run: $ ./faSomeRecords in.exons.fna id-file.txt out.fa faSomeRecords can be downloaded from [here][1] Thank you! [1]: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSomeRecords ...
written 10 months ago by marcelolaia10
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Comment: C: Extract fasta sequences based on ids file
... Hi! > I think if you change $0 ~ pattern to $1 ~ pattern it will give you > the right output. No! It do not solve that behavior . cat id_file.txt | while read id; do grep -A 1 ">$id " seq-file.fasta >> output_file.fasta ; done It is effective in select only the desired IDs, b ...
written 10 months ago by marcelolaia10
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Comment: C: Extract fasta sequences based on ids file
... Yes! I did a search in the forum and found a lot of approaches [here][1]. @Mehmet script is the first one I tried. Second one was @emazep perl [script][2]. I started the perl script yesterday, at night, and it become in a loop until today. It run overnight without end. So, I decided to post a quest ...
written 10 months ago by marcelolaia10
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Extract fasta sequences based on ids file
... I try the script suggested [here][1], but, it retrieve more fasta that is needed. I have: Exon-file.fa >exon-EucgrC_t009-1 transcript=rna-EucgrC_t009 gene=gene-EucgrC_t009 name=trnE-UUC seq_id=NC_014570.1 type=exon ACTG....ACTG....ACTG.....ACTG.....ACTG >exon-NM_001302717.1-11 t ...
fasta perl sequence sed awk written 10 months ago by marcelolaia10
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Comment: C: [Title Edited] How to update the GFF3 wrong file? [was:] featureCounts may be ig
... Hi, `agat_sp_gxf_to_gff3.pl` do the trick! However, is it a possible to see all entries it have been updated? For example, it output in console: Primary tag values (3rd column) not expected => region inverted_repeat sequence_feature cdna_match repeat_region - - ...
written 10 months ago by marcelolaia10
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Comment: C: Different length returned by featureCounts and seqtk comp and AGAT
... Hi @Juke-34. Thank you. I don't will do anything here. Sorry. I will leave it as is. I do that because I am looking for a solution for [this][1]. I need to modify the GFF file to include exon where it isn't there. I'm looking at `agat_sp_gxf_to_gff3.pl`. [1]: https://www.biostars.org/p/436041/ ...
written 10 months ago by marcelolaia10
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Comment: C: Different length returned by featureCounts and seqtk comp and AGAT
... I do a comparison. Here it is. Gene EucgrC_p006, exon 2 https://www.ncbi.nlm.nih.gov/nuccore/NC_014570.1?report=fasta&from=12778&to=13245 NCBI - 468 featureCounts - 468 AGAT - 471 AGAT return the TAG codon, that (may be) is ignored by featureCounts. EucgrC_p021, ex ...
written 10 months ago by marcelolaia10
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Comment: C: Different length returned by featureCounts and seqtk comp and AGAT
... Thank you so much! I will do the changes in my next post. Sorry for that! ...
written 10 months ago by marcelolaia10
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[Title Edited] How to update the GFF3 wrong file? [was:] featureCounts may be ignore chloroplast sequences in a plant genome when use -t exon and -g ID in a GFF file?
... I run featureCounts like this: featureCounts -p -F GFF -a ./NCBI/GCF_000612305.1_Egrandis1_0_genomic.gff -t exon -g ID -o ./featureCounts/A1.counts.txt -f --extraAttributes gene ./raw_data/A1.sam.bam And I extracted exons sequences from whole fasta genome by AGAT like this: agat_sp_extrac ...
forum featurecounts subread rna-seq written 10 months ago by marcelolaia10

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Popular Question 8.3 years ago, created a question with more than 1,000 views. For Retrieve Fasta Sequences From Kegg By Keyword
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