User: marcelolaia
marcelolaia • 10
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- 10
- Status:
- 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
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... 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: ...
written 8 months ago by
marcelolaia • 10
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... 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
marcelolaia • 10
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... 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
marcelolaia • 10
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... 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
marcelolaia • 10
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... 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 ...
written 10 months ago by
marcelolaia • 10
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... 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
marcelolaia • 10
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... 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
marcelolaia • 10
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... 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
marcelolaia • 10
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... Thank you so much! I will do the changes in my next post. Sorry for that! ...
written 10 months ago by
marcelolaia • 10
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... 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 ...
written 10 months ago by
marcelolaia • 10
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