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Hi,
I am getting the
> Can't find any of the first 10 BED transcript_ids in fasta file
error while the transcript_ids of the bed file are clearly in the transcript fasta file.
I parsed the…
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Hello,
What is the format of the exons bed file as input to ichorCNA?
Thank you,
Sudhir
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Hi,
I am trying to generate sashimi plots using BAM files made from running rMATS on FASTQ files. I am using two files that hold my replicates.
My run:
python /Packages/rmats2sashimiplot/src/rm…
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Hello !,
I want to use TOGA for genome annotation and I downloaded the reference genome, but the problem is is that more than 50% of the CDS are not the multiples of 3.
Can you please guide me in t…
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This epic is an umbrella for UTA schema overhaul plans
# Goals:
## Admin changes
* enable schema migrations. This amounts to choosing between keeping SA and using Alembic, or ditching SA (and u…
reece updated
5 months ago
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Dear *,
thank you for sharing your application with the community.
After testing some example cases, I recognized that the exon-exon information is missing or I did not find it.
This information …
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Sorry - not an issue but didn't know where to submit...
Can we also include a column in the tabular file that tells how many exons (i.e., pulls the last exon number in the series for a transcript) th…
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Hello!
I'm working on large cohort with thousands of samples ( > 100 TB). However, due to the limitation of storage, it is not possible to keep all aligned reads at the same time. I found no matte…
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Hello @brianjohnhaas,
I was trying to annotate a StringTie transcriptome assembly, following this pipeline: gtf_to_alignment_gff3.pl -> TransDecoder.LongOrfs -> TransDecoder.Predict -> cdna_alignme…
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Hello,
I tried a multitude of alignment options with a bunch of aligners. I was finally able to find one which can map reads to micro-exons. I fed these alignments, along with the alignments of oth…