User: Ric

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Ric280
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280
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Location:
Australia
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2 days, 17 hours ago
Joined:
7 years, 10 months ago
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m*******@gmail.com

Posts by Ric

<prev • 211 results • page 1 of 22 • next >
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counting the number of reads in FASTQ files
... 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:/ ...
next-gen coverage sequencing written 3 days ago by Ric280 • updated 3 days ago by swbarnes27.0k
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Comment: C: intersecting two GFF3 missing data from the second file
... 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 Ric280
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intersecting two GFF3 missing data from the second file
... 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 ...
bedtools annotation genome written 8 days ago by Ric280
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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 9 days ago by Ric280 • updated 9 days ago by Mensur Dlakic2.1k
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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 5 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 6 weeks ago by Ric280 • updated 6 weeks ago by Juke-342.9k
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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 9 weeks 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 10 weeks 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 10 weeks ago by Ric280
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Comment: C: gene set filter/selection for training ab initio annotation tools
... Thank you for noticing. ...
written 10 weeks ago by Ric280

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For circos plot to compare genomes plot
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