User: Ric

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Ric280
Reputation:
280
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Location:
Australia
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1 day, 13 hours ago
Joined:
7 years, 10 months ago
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Posts by Ric

<prev • 218 results • page 2 of 22 • next >
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Removing adapters for assembly
... 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 ...
assembly abyss written 4 weeks ago by Ric280 • updated 4 weeks ago by Mensur Dlakic2.5k
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Braker2 with filtered BAM files
... 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, ...
gene assembly rna-seq sequencing written 8 weeks ago by Ric280
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StringTie to GFF3
... 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 ...
gene assembly rna-seq written 10 weeks ago by Ric280 • updated 10 weeks ago by Juke-343.1k
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Comment: C: Concatenating default BLAST ouputs
... 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 Ric280
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Concatenating default BLAST ouputs
... 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 ...
alignment blast written 3 months ago by Ric280
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Comment: C: Annotation lifting to a different organism
... 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 Ric280
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Comment: C: gene set filter/selection for training ab initio annotation tools
... Thank you for noticing. ...
written 3 months ago by Ric280
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average distance between genes
... Hi, Is there a way to calculate the average distance between genes and exons from a GFF3 file? Thank you in advance, ...
gene assembly annotation written 3 months ago by Ric280 • updated 7 weeks ago by Alex Reynolds29k
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Comment: C: gene set filter/selection for training ab initio annotation tools
... 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 Ric280
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Comment: C: gene set filter/selection for training ab initio annotation tools
... 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 Ric280

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Popular Question 25 days ago, created a question with more than 1,000 views. For circos plot to compare genomes plot
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