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Hi Sebastian,
Hope all is well. As you already know, we're using Arriba in our pipeline and the more gene fusions data we gather through processing, the more questions we raise :]
We see that fo…
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Hello,
I have a fusion involving a gene which has multiple transcripts. I used the '--examine_coding_effect' parameter to get more information about the detected fusion. I see that the output also…
pwanj updated
3 years ago
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I've written an AGC assembler to learn a little more about the computer. It's based solely on my reading of the original MIT/IL documentation that Virtual AGC has collected, but of course takes yaYUL-…
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It would be great to have the option of running Arriba with the `-I -I` flag so that the calls have a "read_identifiers" column with the supporting read ids; it'll help with checking for alignment art…
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Hi,
First, thank you for the tool, it is a pleasure to use with both ONT and PB data.
I have generated ~29,000 genes with ~130k transcripts in total from multiple datasets using the TAMA pipeli…
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Hi,
I have around 20 samples RNASeq data with ~25Gb data in each sample. Generally, I tend to normalize the dataset for a kmer target depth of 100 at k=25 (using bbnorm/diginorm etc) beforehand so …
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Dear All
I got a list of candidate lncRNAs from FEELnc, but I have some lncRNA which they are matched with exons but plus/minus (according to the blast results) , how I can be determined these ar…
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Hello Brian,
I received the following error during a Trinity assembly, but it seemed to continue. Would you recommend me to stop and restart Trinity?
Best regards
Alfons
which salmon gives…
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Dear BRAPeS developers,
I was trying to run BRAPeS on the example data but had no success. RSEM was installed with bioconda, and the version is 1.3.2.
The error message was "RSEM did not produc…
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I am encountering an error message during trinity run,
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --Running CMD: /home/iipr/trinityrnaseq-2.8.6/Inchwo…