User: mgdias.jose

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mgdias.jose10
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Posts by mgdias.jose

<prev • 18 results • page 1 of 2 • next >
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Comment: C: change specific bases in a fasta file
... I know that it has been a while. This is a very nice solution. But this has one problem. It does not include chromosomes. So, how can it actually find the right position to replace? ...
written 8 weeks ago by mgdias.jose10
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Comment: C: change specific bases in a fasta file
... and for the same position in different chromossomes? ...
written 3 months ago by mgdias.jose10
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Comment: C: bcftools consensus sequence shorter than reference
... Not sure if still on time, but you can try to workaround it by retaining only biallelic sites. Also, you can run a script to remove lines with more than one character in your sequence. This will remove indels. You can do it manually with `awk 'length($REF_column))==1' {print $0}' input.file | awk ' ...
written 4 months ago by mgdias.jose10
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Comment: C: vcf-consensus outputs sequence same as reference
... Do you have multi-samples within the same vcf? If so, try the -s flag ...
written 4 months ago by mgdias.jose10
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Comment: C: Joint variant calling
... If you use the HaplotypeCaller, you should use --ploidy 1. I assume that for bcftools the logic should be similar ...
written 4 months ago by mgdias.jose10
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Comment: C: Samtools (v 1.5) index: failed to create index after sorting by name
... I have the exact same issue. I have alignments generate with mummer4, then converted SAM to BAM view samtools -bT. Finally, the sorting by query name led to the same issue when I have tried to do it with bam files sorted by query name. (Picard SamSort) Just weird the *No such file or directory* mes ...
written 5 months ago by mgdias.jose10
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Comment: C: Samtools Tview Problem
... I found the same behavior (samtools 1.6). In a narrower window, it looked like I had only NN's, but expanding it allowed me to see some alignments. ...
written 5 months ago by mgdias.jose10
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Comment: A: Performing fast bootstrap in R using ape package
... Hello, in the follow-up of the bootstrapping, how can I then draw my actual tree? Does the `boot.phylo` function update the NJ saved in *stree*? In other words, will boot.phylo generate bootstrap trees and update the consensus tree in the variable *stree*? If so, then I could apply `ggtree` on it. ...
written 6 months ago by mgdias.jose10
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Comment: C: Why Is Blast Creating Duplicates In My Output Files?!
... I hae started recently to do a similar type of work and I have noticed the same thing. What I do is a post filtering step where I sort first by lowest e-value and later filter the uniq used ids. ...
written 9 months ago by mgdias.jose10
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Comment: A: BLAST qcov equals to 0
... Can you provide the parameters that you have defined for your blast? ...
written 10 months ago by mgdias.jose10

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