User: jhanks1981

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jhanks19810
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Posts by jhanks1981

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When (not to) pre-build a STAR index
... I am soon to lose my institutional HPC access, and want to port some of my projects to run on a commercial cloud. To avoid excessive costs, I only want to pay when I am using it, and not pay for any more resources than I need. Ideally, I would rent a high memory system for a short period of time in ...
genome-index star written 12 days ago by jhanks19810 • updated 12 days ago by Thibault D.520
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Using Salmon to quantify immature RNA?
... I am looking into using Salmon, but I need to quantify immature transcripts. Salmon examples I have seen all use a transcripts.fa file made of mature transcripts. I was thinking to make a custom transcripts.fa file that includes unspliced transcripts. Is there any reason why this would be a bad idea ...
alignment rna-seq written 5 months ago by jhanks19810 • updated 5 months ago by lieven.sterck5.6k
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Answer: A: RSEM: transcripts.fa.grp not found (should it have been generated?)
... I figured it out. I entered a path to the .fa file where I should have entered the path + name prefix. Seems to work now. ...
written 6 months ago by jhanks19810
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RSEM: transcripts.fa.grp not found (should it have been generated?)
... When I try to run RSEM calculate-expression, it fails with the following error: Cannot open /sc/orga/projects/MetaDope/genomes/rat/rsemRef/rat.transcripts.fa.grp! It may not exist. I checked in the rsem reference folder and sure enough there is no rat.transcripts.fa.grp. There is a rat.grp how ...
rna-seq rsem written 6 months ago by jhanks19810
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Comment: C: Why can't I use a GRanges txDb with clusterMap function? (as input or output)
... Apologies if this is a naive question, but is that something I can do something about? ...
written 20 months ago by jhanks19810
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Why can't I use a GRanges txDb with clusterMap function? (as input or output)
... I need to create several transcript database objects from different GTF files, so I would like to save time by running each txdb creation in parallel. However, the txdb that is generated when I have run it in parallel (although it completes without errors) doesn't behave like the one generated by ...
R parallel genomicfeatures clustermap written 20 months ago by jhanks19810
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Comment: C: Custom features in IGV
... Interesting. I am on version 2.3.97 for Linux. Is there a better/more consistent viewer than IGV? ...
written 2.0 years ago by jhanks19810
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Comment: C: Custom features in IGV
... I will try that. Strange though, I've used GTF files with other feature types ("gene", "transcript") without issue. Also, I was reading about the GTF format from here: http://www.ensembl.org/info/website/upload/gff.html Edit: Yes, that did the trick. Thanks! ...
written 2.0 years ago by jhanks19810
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Comment: C: Custom features in IGV
... Sorry, the link was in the raw post, but for some reason it didn't show. The "Custo," was supposed to be "Custom". ...
written 2.0 years ago by jhanks19810
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Custom features in IGV
... I am making gtfs file with custom feature types, and I want to inspect them in IGV viewer. However, I cannot view the features if they have a non-standard attribute type (INTRON). However, if I replace the string "INTRON" with "exon", the file displays as expected. Is IGV viewer unable to display an ...
gtf features igv written 2.0 years ago by jhanks19810 • updated 2.0 years ago by Dan D6.8k

Latest awards to jhanks1981

Scholar 6 months ago, created an answer that has been accepted. For A: RSEM: transcripts.fa.grp not found (should it have been generated?)

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