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Hi,
I am working with Rat genome and I have downloaded the files cdna and ncrna as directed and followed the steps of merging them together but I did not filter them for anySuper contig or haplotype …
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The transcript names in Gencode's reference sequence fasta files have the following format:
ENST00000257408.4|ENSG00000134962.6|OTTHUMG00000128577.1|OTTHUMT00000250429.1|KLB-001|KLB|6082|UTR5:1-97|CDS…
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I've switched to using precompiled binaries, version 0.6.0. Now working on a new server running CentOS Linux release 7.1.1503. I was able to successfully generate my index, then started running the …
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Hi, I really like salmon, it's really fast. Somehow I need FPKM rather than TPM. I got the output with 3 values out: Length, TPM and NumReads.
In RSEM, they have both length (which equal to the length…
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Hello All,
I wanted to know if I can use Sailfish for single replicate study for three different conditions.
Thank you!
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I am intending to run salmon on a set of RNA-Seq data lying in our lab for a long time. They are for mm9 and since there are >50 samples I was intending to run it using Salmon `version : 0.6.0`. I hav…
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Hi, I was trying to investigate a thing using the Gibbs samples (and bootstraps).
I vaguely recall seeing both issues I'm reporting here somewhere, but I can't find those by searching.
I used Salmon…
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Hi There,
I am trying to build the index for gencode transcripts but all versions of sailfish give a failure error at the end. Here's the transcripts I get when I run the index:
sailfish index -t ge…
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Hello @roryk and crew, I was wondering whether the current RNA-Seq pipeline still is depending on quality/adapter/poly-a trimming or if this step could be left out (since it produces quite some extra …
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Dear IsoSCM developers,
I've successfully run assembly command and what to compare differential 3'UTR usage in my dataset. When I run compare command I get the following traceback:
2015-05-27T12:07:…