User: vmicrobio

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vmicrobio240
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Posts by vmicrobio

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Answer: A: Contig longer than mitochondrial sequence. Explanation ?
... You may have some similar patterns in your mitochondrial which will generate errors during assembly. What de novo assembler did you used? which parameters? You may try more stringent parameters or another software ...
written 7 days ago by vmicrobio240
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how to highlight hotspot rearrangments regions?
... Hello biostars community I would like to understand what happened in a human genome containing some complex rearrangements. I would like first to focus on a/some region/s containing potentially rearrangements and then look deep at the hybrid reads present in this particular region. However there a ...
hybrid reads rearrangment hotspot region written 8 days ago by vmicrobio240
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Comment: C: count number of references with at least one hit
... and `wc -l` output file ...
written 3 months ago by vmicrobio240
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Comment: C: count number of references with at least one hit
... I had to format a little bit the heads of multifasta file but it works. Thanks a lot! ...
written 3 months ago by vmicrobio240
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Comment: C: count number of references with at least one hit
... I just would like to get the information : on X references Y are mapped by at least one read. Do you think I should go with idxstats output? ...
written 3 months ago by vmicrobio240
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count number of references with at least one hit
... Hello, In a context of mapping reads with multireferences, I was wondering how to count number of references with at least one hit (and not number of reads matching with ref). A way would be to make a custom script with files obtain from `samtools idxstats` after alignment. Is there a `samtools` c ...
alignment references written 3 months ago by vmicrobio240 • updated 3 months ago by Pierre Lindenbaum126k
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Comment: C: differences between bwa-mem paired and single reads
... thank you for your comment. You're right, percentages are ratio between mapped and total reads, and 3 and 97% are no real values but more a global average for all samples. For one random sample : 3.03% for hg19, 96.3% for virus, so 0.67% are non mapped. Here are the outputs of `samtools flagstat` : ...
written 7 months ago by vmicrobio240
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differences between bwa-mem paired and single reads
... Hi! I would like to highlight hg19/virus ratio for Illumina paired reads. My first step was to remove hg19 reads (using `-f4 samtools`) and then align remaining reads against virus. I have noticed that using the same parameters I got different results for same run if I process paired reads (50% h ...
alignment bwa written 7 months ago by vmicrobio240
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Answer: A: How to download all the genome sequences (including draft and complete) of a par
... I'll try something like this: /../edirect/esearch -db nucleotide \ -query "Xanthomonas[organism] AND genome[title]" \ | /../edirect/efetch -format fasta > allXanthomonas.fasta then makeblastdb -in allXanthomonas.fasta -parse_seqids -dbtype nucl -title xanthomonas -o ...
written 12 months ago by vmicrobio240
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Comment: C: How can I make a .bed file from my fasta?
... are your sequences located on the genbank? if so, you can retrieve genebank files and execute a script such as : #!/usr/bin/env python # encoding: utf-8 """ bed_from_genbank.py grab the gene records from a genbank file (edit for other record types). - requires ...
written 16 months ago by vmicrobio240

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