User: rbronste

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rbronste80
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Posts by rbronste

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Calculating FPKM values from HT-counts
... I believe you're right. Giving the script you linked a shot as well. Just so I understand completely what is background fasta you're using here? Also in this instance the GC length is being used as a proxy for transcribed length? Thanks for the help! ...
written 7 days ago by rbronste80
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Comment: C: Getting avg gene length from GTF (for all splice isoforms)
... I have it in the originally exported from UCSC format, refSeq GTF file of gene components. However get a similar error to before with the suggested awk command: awk: fatal: division by zero attempted ...
written 7 days ago by rbronste80
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Comment: C: Getting avg gene length from GTF (for all splice isoforms)
... Using version: 2.4.25 ...
written 7 days ago by rbronste80
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Comment: C: Getting avg gene length from GTF (for all splice isoforms)
... The first two steps work well after installing and running the fetchChromSizes bash script. However getting the following error when trying the gtf2bed: *** Error in `convert2bed': realloc(): invalid next size: 0x0000000000bcf390 *** /sonas-hs/smith/hpc_norepl/home/software/bedops/bin/gtf2bed: line ...
written 8 days ago by rbronste80
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Getting avg gene length from GTF (for all splice isoforms)
... Hi, Just looking for a way to get avg gene length from a GTF file acquired from UCSC table browser. At this stage not looking at alternative transcripts. Thanks. Rob. ...
table browser gtf rna-seq ucsc written 8 days ago by rbronste80 • updated 8 days ago by Alex Reynolds19k
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Comment: C: Calculating FPKM values from HT-counts
... I usually do as well, just wondering if it was just somewhere in UCSC. I usually do the following in R: library(GenomicFeatures) txdb <- makeTxDbFromGFF("test.gtf", format="gtf") trans <- transcripts(txdb, columns=c("GENEID")) df <- data.frame(gene=trans$GENEID, len=width(trans)) I am won ...
written 8 days ago by rbronste80
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Comment: C: Calculating FPKM values from HT-counts
... Great thanks, any particular place its easiest to download list transcript lengths? I guess UCSC table browser? ...
written 8 days ago by rbronste80
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Comment: C: Setting up a lab wiki
... I guess in my question I am even looking for something simpler since I am the primary person in the lab doing bioinformatics. Just wanted a place to easily and quickly share workflows and pipelines. ...
written 11 days ago by rbronste80
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Setting up a lab wiki
... Hi everyone, Wondering about how laboratories out there that pursue wet lab work as well as bioinformatics centralize their computational protocols and pipelines. I am considering setting up such a centralized resource for my lab, where everyone doing data analysis can submit minute detailed aspect ...
wiki data analysis and organization written 12 days ago by rbronste80 • updated 12 days ago by Jean-Karim Heriche10k
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Calculating FPKM values from HT-counts
... Hi, Interested in converting some raw HT-counts to FPKMs and wondering how everyone approaches this problem? I have a few ideas but was interested in the consensus view. Thank you! Rob. ...
rpkm fpkm rna-seq written 13 days ago by rbronste80 • updated 13 days ago by Devon Ryan66k

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Rising Star 24 days ago, created 50 posts within first three months of joining.
Supporter 26 days ago, voted at least 25 times.

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