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Hi Alex,
Apologies if this question has already been asked and answered. I've searched but haven't found it.
I have 2x151 bp data.
Perfectly aligned fragments (no mismatches) without …
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I think hisat is not handling ribosomal RNA reads very well (see image). Neither are Star or Tophat2.
Tophat also finds a bunch of strange splice junctions (top)
Hisat is finding a bunch of splice jun…
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```
Hi,
I'm trying to figure out how to run a second mapping pass, as described in the
paper
"It is also possible to run a second mapping pass, supplying it with splice
junction loci found in the …
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@infphilo
I was wondering if there is a way I can generate junctions.bed file from hisat2 just like the one in tophat.
Hisat2 documentation says use extract_splice_site.py python script but tha…
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**Copy and paste the exact command you tried to run**
```
flair correct \
-q /bed_data/$query_bed12 \
-f /genome_data/$annotation \
-g /genome_data/$genome \
--output /bed_data \
--threads 16 \…
-
```
Hi,
I'm trying to figure out how to run a second mapping pass, as described in the
paper
"It is also possible to run a second mapping pass, supplying it with splice
junction loci found in the …
-
Include IGV Sashimi plot as a component. We'd like to reuse this element in Mosaic as well. Here is the issue from Mosaic:
This looks to be at least partially possible based on this wiki [here](htt…
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Hi,
I am using single end library for my differential splicing analysis. As I use regtools (version 0.5.2, -s 2) to generate junc files it recognize junctions on one strand and not the other. There…
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### Description
Right now, the outrigger output is a big nested mess:
```
$ tree outrigger_output
outrigger_output..........................................................index
├── index....…
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Thanks for this tool. I find my self wanting to quantify SplicingEfficiency of unannotated introns. I was wondering if there is any chance you would implement this, perhaps by accepting user defined l…