User: mgdias.jose

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Posts by mgdias.jose

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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 4 weeks ago by mgdias.jose0
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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 4 weeks ago by mgdias.jose0
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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 12 months ago by mgdias.jose0 • updated 12 months ago by WouterDeCoster35k
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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 12 months ago by mgdias.jose0
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... My problem here is that I want to make comparisons within the same assembly, but just different releases. And for that none of these tools will work. Or is there any way to do it? Thank you ! ...
written 12 months ago by mgdias.jose0
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Answer: A: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... Hello, thankyou for the amazing work compiling all these different tools. For what I got, most of this tools work well between different assembly versions (let's say 37 vs 38), BUT if I want to compare data within the same assembly but different releases do you have any suggestion of the best app ...
written 12 months ago by mgdias.jose0
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Comment: C: Reannotate genomic data with new Ensemble release
... Hello, my data is in mouse and therefore, there is only possible to assemble Ensembl vs NCBI and it is in txt format. Do you know any other platform/tool? Is there any way to convert it to one of those file formats without losing configuration ? Thanks ...
written 13 months ago by mgdias.jose0
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Reannotate genomic data with new Ensemble release
... 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 assemb ...
gene ensembl transposon annotation data written 13 months ago by mgdias.jose0 • updated 12 months ago by Sean Davis25k

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