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I see that there exist circular RNA support in Sailfish ( http://www.rna-seqblog.com/tag/sailfish-cir/ ), maybe it will be beneficial to see a Salmon port of it?
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Hey,
Thanks for sharing this amazing tool!
I found that **chrMT** appears in the .bed and .junction files, but not in the final counts table.
I was wondering if there is any way to help me gen…
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I tried both circtools detect v1.3.1 and DCC v0.5.0 using this command in Snakemake:
I only used one sample, paired-end read
```
circtools detect {input.samplesheet} \
-mt1 {input.…
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I noticed that the command to extract intron in this script does not seem to be able to correctly generate the gtf file of intron.
As shown in the figure below, the intron interval extracted from the…
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Hi egaffo,
I'm trying to run circompara on my samples, but I got the following error:
finished circRNA detection from file samples/S1/processings/circRNAs/star_out/Chimeric.out.junction
dcc_fix_s…
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Hi Egaffo, I have the following error:
"[SEGEMEHL] Fri Dec 29 08:21:58 2023: starting 65 threads.
[SEGEMEHL] Fri Dec 29 18:04:02 2023: threaded matching w/ suffixarray has taken 34924.000000 seconds…
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When I run the test, whether `cd test_circompara/analysis
../../circompara2` or `cd test_circompara/analysis_se
../../circompara2` , it reported this error.
I install circompara2 in conda python=2.…
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Hello, I have the following error:
scons: *** [samples/S4/processings/circRNAs/tophat_out/accepted_hits.bam] Error 1
which appears during the tophat process.
Indeed I have the following:
[2023…
npont updated
11 months ago
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- [ ] Align the data as necessary for circtools:DCC, using the genome index:
```
/reference/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/
```
and the de-novo assembled gene annotation:
`…
plger updated
5 years ago
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Hi Kipp,
I have met another issue when I analyzed my data (stranded total RNA-Seq) from FASTQ files. Only 9 circRNAs were detected but previously using BAMs as the starting point I found more than …