User: mgdias.jose

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mgdias.jose10
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Posts by mgdias.jose

<prev • 14 results • page 1 of 2 • next >
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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 17 days 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 23 days 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 4 weeks 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 11 weeks 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 5 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 5 months ago by mgdias.jose10
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Comment: C: Did anyone manage to successfully run HLAScan and get results?
... Did you get any answer? I have the exactly same problem. In the Mac terminal I was not able to run it and after changing to Ubuntu, I always end up with the 'HLAscan cannot determine proper types' message ...
written 12 months ago by mgdias.jose10
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Comment: C: Did anyone manage to successfully run HLAScan and get results?
... Inside the zipped file from the url provided by @airexpend inside of data-set/db/ folders named HLA-ALL.IMGT. just addd it in front of -d command. $ ./hla_scan -l NS_L001_R1_001.fastq.gz -d data-set/db/HLA-ALL.IMGT -g HLA-A ...
written 12 months ago by mgdias.jose10
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(Closed) Reannotete/Compare data between ensembl releases but within the same assembly
... I have transposons data for mouse organised in the following manner (txt) chr start end hit 1 111 130 geneXXX 2 1546 1867 intergenic 3 123 234 geneYYY this is for the assembly 38, Ensembl release 73. I want to compare it now with the release 90 of Ensembl (which is still ...
ensembl reannotation mouse transposon written 24 months ago by mgdias.jose10 • updated 24 months ago by WouterDeCoster42k
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... I have transposons data organised in the following manner (txt) chr start end hit 1 111 130 geneXXX 2 1546 1867 intergenic 3 123 234 geneYYY this is for the assembly 38, Ensembl release 73. I want to compare it now with the release 90 of Ensembl to confirm if the hits of ...
written 24 months ago by mgdias.jose10

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