Open HosseinAsghari opened 4 years ago
Hi,
Please provide the following information:
thanks, tw
Hi,
Log files: ncls.log.txt ncls.out.txt
Hossein
Hi,
If you don't mind, please send me the file "all.out.JS2.sam" in the NCLscan output directory.
And could you try the test dataset mentioned in the README? I was wondering if it could be run successfully.
the following is the link to the test dataset:
Thanks, tw
Hi again and thanks for the follow up.
Here is the file you requested.
And yes, I have tested the sample dataset. It runs without any problems and produces results.
Hossein
Hi,
This issue should be due to the behavior changes of novoalign V4.
The option "--pechimera", which is used to enable the use of supplementary alignments when one read of a pair is chimeric, changed its default value to "on".
This change would break the NCLscan pipeline.
The following was found in the file "all.out.JS2.sam",
simulate:8826 99 simulate:8847.0 89 0 63S38M = 275 287 TTCGGCCTCTACCCAAAGTGAAAAGACTGCTGTCAGATAGCACTTGCCTTCCCCATATTATTCAGAAAAATGTTAAGGATCTCATGGATTCAAATGGAATA 55555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555 PG:Z:novoalign AS:i:0 UQ:i:0 NM:i:0 MD:Z:38 PQ:i:8 SM:i:0 AM:i:0 ZS:Z:R NH:i:10 HI:i:1 IH:i:1 Z3:i:126 SA:Z:simulate:8847.6,931,+,63M38S,3,0;
simulate:8826 147 simulate:8847.0 275 0 101M = 89 -287 GTGGCCCGTATGGATTTCATGAGATGCAAGAATTGTGGACCAAAGGAATGTTAAATGCAAAAACCAGATGCTGGGCTCAAGGCATGGATGGATGGCGACCA 55555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555 PG:Z:novoalign AS:i:0 UQ:i:0 NM:i:0 MD:Z:101 PQ:i:8 SM:i:0 AM:i:0 ZS:Z:R NH:i:10 HI:i:1 IH:i:1 Z3:i:375
simulate:8826 2145 simulate:8847.6 931 3 63M38S simulate:8847.0 275 0 TTCGGCCTCTACCCAAAGTGAAAAGACTGCTGTCAGATAGCACTTGCCTTCCCCATATTATTCAGAAAAATGTTAAGGATCTCATGGATTCAAATGGAATA 55555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555 PG:Z:novoalign AS:i:0 UQ:i:0 NM:i:0 MD:Z:63 ZS:Z:R NH:i:10 HI:i:1 IH:i:1 Z3:i:993 SA:Z:simulate:8847.0,89,+,63S38M,0,0;
The parser in NCLscan pipeline needs these alignments to be ordered by pairs, but these additional rows would break it.
--
For now, you could just use novoalign V3 to avoid this problem.
And we should fix this in the future.
Thanks! tw
Hi,
I am trying NCLscan on some paired-end data and the run finishes with the following message:
However, "out.result" is an empty file while I expect to get many circRNAs.
At the end of the standard error output I got a bunch of "Format Error!" and a few "Format Error! Not paired-end!".
Here is the list of output files: output.list.txt
I was wondering what would be the reason of this issue.
Thanks in advance, Hossein