User: Ric
Ric • 290
- Reputation:
- 290
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- Location:
- Australia
- Last seen:
- 1 day, 11 hours ago
- Joined:
- 8 years, 1 month ago
- Email:
- m*******@gmail.com
Posts by Ric
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... Thank you. By any chance, do you have a summary of rules when genes will be considered or not? ...
written 2 days ago by
Ric • 290
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... Thank you, I noticed that `agat_sp_complement_annotations.pl` did not remove overlapping genes as shown in my updated question in the top. What did I miss?
Thank you in advance ...
written 2 days ago by
Ric • 290
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... HI
# Please report
$ abyss-pe version
abyss-pe (ABySS) 2.2.4
$ lsb_release -d
Description: Ubuntu 18.04.1 LTS
# Assembly error
**complete `abyss-pe` command line**
export TMPDIR=/mnt/volume1/abyss-96-fastp/tmp
mkdir $TMPDIR
abyss-pe k=96 name=16c-96 lib='pea p ...
written 3 days ago by
Ric • 290
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... Hi,
I would like to only unique mapped paired-end reads. Reads which are not anymore in pair I would like to remove. After the the below steps the BAM file did not contain any reads anymore:
1. aligned pair-end data with bowtie2.
2. Removed duplicates with MarkDuplicates
3. kept aligned reads ...
written 7 days ago by
Ric • 290
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... Hi,
I am using the below script to merge around 1000 BAM files. However, the merged file is tiny compare to each separately BAM files.
> sh split_bam2sam-fasta_pbs.sh bams-1/*.q40.FixMate.clean.bam
bams-1/t_correction.0.fq.sorted.bam.dedup.q40.FixMate.clean.bam bams-1/t_correction.100.f ...
written 9 days ago by
Ric • 290
• updated
9 days ago by
Pierre Lindenbaum ♦ 126k
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... Hi, Does anyone knows cheap and good Hi-C protocols? Our focus is on plants.
Thank you in advance,
...
written 13 days ago by
Ric • 290
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... While using agat to convert to protein I got:
(In case your file contains only CDS features, and your organism is prokaryote (e.g rast file), using ID as comon_tag might be the solution.)
13 warning messages: Peculiar rare case, we found 8 three_prime_utr while 12 expected.
Either ...
written 18 days ago by
Ric • 290
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... I ran `gff3_sp_complement_annotations.pl --ref stringtie.gff3 --add augustus.hints_utr.gff3 --out gaas.gff3` and got the below new IDs:
NbV1Ch01 transdecoder five_prime_UTR 99705 99705 . - . ID=nbis_NEW-five_prime_utr-4254;Parent=STRG2.t1
NbV1Ch01 tr ...
written 20 days ago by
Ric • 290
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... I have an annotation file in GFF3 format, but I do not have the amino acid and cds sequences any more. Is there a tool which can retrieve those files from a genome in FASTA format and a GFF3 file?
Thank you in advance ...
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