User: Ric
Ric • 280
- Reputation:
- 280
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- Location:
- Australia
- Last seen:
- 1 day, 13 hours ago
- Joined:
- 7 years, 10 months ago
- Email:
- m*******@gmail.com
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... Hi,
I ran fastp with this parameters `fastp --detect_adapter_for_pe --correction ... ` and it removed the adapters and trimmed the paired-end reads. Which read length should I remove form the below read length distribution?
#count #lenght
329 15
552 16
503 17
...
written 4 weeks ago by
Ric • 280
• updated
4 weeks ago by
Mensur Dlakic • 2.5k
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... Hi, I was thinking after HiSAT2 to run MarkDuplicates and remove aligned reads with lower than 40 quaily score. Then to run BRAKER2 with the filtered reads.
Did anyone try it and did it improve the annotation?
Thank you in advance, ...
written 8 weeks ago by
Ric • 280
3
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... Hi,
I ran StringTie and converted its results to GFF3 with the following commands:
> gffread -E stringtie_merged.gtf -o- > stringtie_merged.gff3
> sed -i.bak 's|transcript|mRNA|g' stringtie_merged.gff3
##gff-version 3
NbV1Ch01 StringTie mRNA 212226 219213 ...
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... I tried to use `bp_search2gff.pl` (part of BioPerl) which only supports the pairwise BLAST output. The goal is to speed up tBLASTn. ...
written 3 months ago by
Ric • 280
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... Hi, I split my FASTA file into many chunks and ran BLAST with default settings against a database. Is there a way to concatenate default BLAST outputs?
TBLASTN 2.3.0+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Mil ...
written 3 months ago by
Ric • 280
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... I used the following additionally steps:
> sed 's|,AT.*-Protein;||g' TAIR10_GFF3_genes-fix1.rm_rubbish_rm_protein.gff > TAIR10_GFF3_genes-fix1.rm_rubbish_rm_protein_rm_id.gff
> echo "##gff-version 3" > TAIR10_GFF3_genes-fix1.rm_rubbish_rm_protein_rm_id_rm_index.gff
> ...
written 3 months ago by
Ric • 280
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... Thank you for noticing. ...
written 3 months ago by
Ric • 280
1
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... Hi,
Is there a way to calculate the average distance between genes and exons from a GFF3 file?
Thank you in advance,
...
written 3 months ago by
Ric • 280
• updated
7 weeks ago by
Alex Reynolds ♦ 29k
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... It seems to work for now after `sed 's|,AT.*-Protein;||g' TAIR10_GFF3_genes-fix1.rm_rubbish_rm_protein.gff > TAIR10_GFF3_genes-fix1.rm_rubbish_rm_protein_rm_id.gff`. ...
written 3 months ago by
Ric • 280
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... I would like to keep those features because they mRNA contain `Note` (writing into keep.gff3 file)
NbV1Ch08 AUGUSTUS gene 60876 63944 0.03 + . ID=g2
NbV1Ch08 AUGUSTUS mRNA 60876 63944 0.03 + . ID=g2.t1;Note=B3 domain-co ...
written 3 months ago by
Ric • 280
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