User: Ric
Ric • 280
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- 2 days, 17 hours ago
- Joined:
- 7 years, 10 months ago
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Posts by Ric
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... Hi, I would like to get the read coverage and I found [here][1] C = LN / G whereas:
- C stands for coverage
- G is the haploid genome length
- L is the read length
- N is the number of reads
How is it possible to count the number of reads in FASTQ files?
Thank you in advance
[1]: https:/ ...
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... Thank you for your explanation. I think the output from your script is correct if mRNA has an opposite strand. However, do you think that mRNA with `g83526.t1` might be affected by the UTR rule (![screenshot][1]):
> grep "g83526.t1" augustus.hints_utr.gff3
NbV1Ch03 AUGUSTUS mRNA 68949416 ...
written 5 days ago by
Ric • 280
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... Hi,
I have both StringTie (*stringtie_merged.gtf.fasta.transdecoder.genome.gff*3) and BRAKER2 (*augustus.hints_utr.gff3*) GFF3 files which I would like to intersect with bedtools. Whenever StringTie covers the genome region and BRAKER2 intersect them then I would like to remove BRAKER2 annotation. H ...
written 8 days ago by
Ric • 280
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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 9 days ago by
Ric • 280
• updated
9 days ago by
Mensur Dlakic • 2.1k
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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 5 weeks ago by
Ric • 280
3
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1
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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 9 weeks ago by
Ric • 280
1
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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 10 weeks ago by
Ric • 280
0
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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 10 weeks ago by
Ric • 280
0
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262
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... Thank you for noticing. ...
written 10 weeks ago by
Ric • 280
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For estimate genome coverage
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