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Hi Alex,
Encountered a strange error while running star current version and previous 2.5a as well.
EXITING because of FATAL ERROR: phtread error while creating thread # 8, error code: 11
Do you kn…
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Bonus score should be given to transcripts who have supported introns. In order to do this, support will need to be extracted from the RNAseq hints db.
Possible way for this to work: weighted score =…
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HISAT is not outputting splice junctions. Regtools will be wrapped and added into toolshed.
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**Issue**
This option Coverage Search (under full params) is marked as "No" by default, yet is not included in the command-line. This causes certain jobs to fail (likely for resource) but the error o…
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When I run the test data with default options I get the error message "trimfq: invalid option -- 'B'". If I add the option --5keep 0 to stop trimfq, everything is OK (so far). I believe the following …
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Hi,
I am currently going through some RNA-seq data using QoRTs and JunctionSeq. I have been very impressed with JunctionSeq and the amount of visualisation it produces to help interpret the data.
Th…
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I'm trying to convert [exonerate](http://www.ebi.ac.uk/~guy/exonerate/) output to psl using a simple script:
``` python
from Bio import SearchIO
QRESULTS = SearchIO.parse("my_exonerate.out", 'exonera…
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This seems a bug in the file opening. Error:
```
bash-4.2$ head -n 3 junc/portcullis.junctions.tab
index refid refname reflen start end left right ss1 ss2 read-strand ss-strand consensu…
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A qorts run on my standard pipeline works. A standard pipeline is index clipped paired-end fastq files mapped to indexed genome using star and then running qorts on the bam file (pos sorted) using the…
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Hello!
Thanks very much for the effort in developing QoRTs and JunctionSeq. I'm very enthusiastic about the results I've obtained and will shortly validate some of the output via qRT-PCR. However, I …