User: alex.zaccaron

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alex.zaccaron120
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Posts by alex.zaccaron

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Extract N amino acids from fasta file
... Yes, it does. Sorry, I thought the input file was tabular format. I updated the comment. ...
written 6 weeks ago by alex.zaccaron120
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Comment: C: Extract N amino acids from fasta file
... You could convert to tabular format with `seqkit` and use the substring function from `awk`: seqkit fx2tab file.fasta | awk -v FS="\t" '{print ">"$1"\n"substr($2,1,30)}' ...
written 6 weeks ago by alex.zaccaron120
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Comment: C: Why map reads back to assembly?
... Mapping reads back to the genome is useful to check completeness: you would expect ~99% of reads mapped, depending on your sample. Also, it can be used to detect collapsed regions, usually repetitive DNA, by identifying high coverage regions: for example >3 times the average. ...
written 10 weeks ago by alex.zaccaron120
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Comment: C: Polish PacBio assembly with Hi-C reads
... I gave it a shot, but did not move forward with it. Based on the info I gathered, it can be done but there is no guarantee of the results. At the end, we decided to sequence more Illumina data for the polishing step to avoid downstream problems. But I can still describe what I did: To polish the as ...
written 10 weeks ago by alex.zaccaron120
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Comment: C: How to minimize chimeric transcripts assembled with StringTie
... Seems like erroneously predicted UTRs could be a problem. The reconstructed transcripts look better when I removed the gene UTRs from the annotation (shown [here][1]). [1]: https://i.ibb.co/cTN9nq6/Picture2.png ...
written 3 months ago by alex.zaccaron120
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How to minimize chimeric transcripts assembled with StringTie
... Hello, I am working on a non-model fungal organism and I am trying to assemble transcripts with StringTie based on RNA-seq reads mapped to the assembled genome. My ultimate goal is to perform differential expression analysis at the transcript level. However, I noticed some cases where StringTie mer ...
stringtie rna-seq transcriptome written 3 months ago by alex.zaccaron120
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Comment: C: Assembly statistics: abyss & bbmap
... You can change the parameter `n` within `stats.s` to adjust the required number of contiguous Ns in order to consider the sequence a scaffold instead of a contig. For example, if you specify `n=1` then `stats.sh` will "break" a contig at every single N. I am not sure what ABySS considers, but has to ...
written 3 months ago by alex.zaccaron120
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Comment: C: Assembly statistics: abyss & bbmap
... Keep in mind that, by default, BBmap `stats.sh` requires at least 10 consecutive Ns between two contigs to consider it a scaffold. Also, `stats.sh` is likely considering all contigs/scaffolds to calculate N/L50. Usually, contigs shorter than 250 or 500 bp are remove from draft assemblies, and I thin ...
written 3 months ago by alex.zaccaron120
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Comment: C: Converting an output de-novo transcriptome assembled with Trinity to a .gff3 fil
... I do not have experience with Trinity, but I have seen similar cases where a GFF3 was obtained by mapping the Trinity fasta to the reference with [GMAP][1]. Maybe it can help in your case. [1]: https://anaconda.org/bioconda/gmap ...
written 4 months ago by alex.zaccaron120
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Answer: C: Filtering BED file for interval length
... `awk` should work fine: awk '{if($3-$2 <= 1000) print}' file.bed > file_filtered.bed ...
written 4 months ago by alex.zaccaron120

Latest awards to alex.zaccaron

Scholar 4 months ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Fasta extraction from bed file
Scholar 5 months ago, created an answer that has been accepted. For C: Fasta extraction from bed file
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: Fasta extraction from bed file

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