-
Hi,
I am running into a weird behavior when running STAR with the option `--quantMode TranscriptomeSAM` to obtain a bam file in transcriptome space.
My transcriptome is somewhat non-standard as I…
-
Hi, I need help with an error running rpvg command.
I'm getting "paths_index.cpp:73: uint32_t PathsIndex::nodeLength(uint32_t) const: Assertion `hasNodeId(node_id)' failed" error, but I have no idea …
-
Hello all,
Thanks for this really nice tool - I am having trouble with my analysis and am hoping someone can tell me what is going on here. I am using hte same pipeline as I did a couple of years a…
AAA-3 updated
1 month ago
-
I'd like to extract reads from a .gam file that do not align to any nodes that are in a reference path. My end goal is to identify coverage and depth of likely insertions.
Commands that strike me a…
-
Dear Shun,
Thank you for the eTAM workflow.
After running the trim step, I get fastq results empty.
I also want to inquire about some details about the mapping step.
Here are my workflow d…
ghost updated
10 months ago
-
Hi,
I have a stringtie output in gff3, but parsing with gff3_validator, it provides me the following output:
Fatal Error: cannot parse ID from entry
Scaffold_2 StringTie exon 38612 …
-
We have some larger bam files 40-90GB aligned with Hisat2, that are merged from 3 replicates of the same sample that we've been running stringtie on. We're using version 1.3.3b on RHEL7 with 128GB …
-
Hi there,
I have long read RNA-seq data from the minion platform. I'm trying to plot gene body coverage of these reads. Is there a reason this data wouldn't be compatible with the QoRTs java applica…
-
Hi Brian.
I've moved on to EVM after talking with you about TransDecoder yesterday. I'm trying to use Exonerate protein2genome alignments from a Maker run as input to EVM. I'm am wondering about ge…
-
Hi, I have some questions about using RMATS
1. If I only want to test how much AS is contained in a sample (containing 3 biological replicates) instead of differential variable shear, the followin…