User: Ric

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Ric290
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

<prev • 249 results • page 1 of 25 • next >
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Comment: C: gff3_sp_complement_annotations.pl parameter settings
... Thank you. By any chance, do you have a summary of rules when genes will be considered or not? ...
written 2 days ago by Ric290
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Comment: C: gff3_sp_complement_annotations.pl parameter settings
... 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 Ric290
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sparsehash FATAL ERROR: failed to allocate 19 groups
... 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 ...
assembly abyss written 3 days ago by Ric290
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no unique mapped paired-end reads in BAM file
... 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 ...
ngs alignment sequencing written 7 days ago by Ric290
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samtools merge not working
... 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 ...
alignment next-gen samtools sequencing written 9 days ago by Ric290 • updated 9 days ago by Pierre Lindenbaum126k
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(Closed) cheap and good Hi-C protocol
... Hi, Does anyone knows cheap and good Hi-C protocols? Our focus is on plants. Thank you in advance, ...
assembly next-gen sequencing written 13 days ago by Ric290
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Comment: C: How to retrieve from a GFF3 file a AA and CDS files
... 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 Ric290
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Comment: C: gff3_sp_complement_annotations.pl parameter settings
... Thank you, I used it. ...
written 19 days ago by Ric290
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gff3_sp_complement_annotations.pl parameter settings
... 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 ...
gene annotation written 20 days ago by Ric290
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How to retrieve from a GFF3 file a AA and CDS files
... 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 ...
gene annotation written 22 days ago by Ric290 • updated 22 days ago by Juke-343.3k

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