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Dear team,
I'm a little bit confused about the build index step. The manual says that it builds a transcriptome index but needs as input a genomic fasta and a gff. I would like to create the count…
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Genome based transcriptome assemblers like Cuflinks produce large no of transfrags. Are these real? if not, they are likely to impair differential expression analysis of isoforms adding more confusion…
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Hello,
I would like to run factR2 on a custom assembly where I ran in the issue described in [https://github.com/f-hamidlab/factR2/issues/7](issue#7). So I thought I try it on the example data you …
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Dear Team,
I run Whippet on my paired-end, unstranded, polyA+ RNA-seq dataset. The dataset is of 75bp length (all reads in all samples have this length) and performed in triplicates per condition (…
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### Ask away!
Dear community,
I am quite new to this, I have performed a transcriptome analysis using epi2me labs app,
My question is, what should i do after ? I have several files and I don't k…
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I am trying make a Salmon Indexing but when I run with this code:
$salmon index -t ../transcriptome/gencode.v37.transcripts.fa.gz -i ../transcriptome/genecode.v37.salmon141
And I got this erro…
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I got this issue.
We are sorry, commands in file: [FailedCommands] failed. :-(
Error, cmd: /flask/apps/eb/software/Trinity/2.2.0-foss-2016b/trinityrnaseq-2.2.0/trinity-plugins/parafly/bin/ParaFl…
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Hello,
We've produced in vivo probing data (SHAPE treated and untreated) to study transcriptomic structures, but shapemapper2 doesn't natively output reactivity data for entire transcriptome. We've …
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I'm getting segmentation faults thrown with one transcriptome, tried running both blastx and blastp and both fail. See here for the files:
https://drive.google.com/file/d/1v2f7wH-6G4MvFERaaZ96aDeFJjT…
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Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment