Question: MapSplice Error: filter alignment failed
0
gravatar for liguanghaoli
5 days ago by
liguanghaoli0 wrote:

Hi, When I use MapSplice to do mapping in RNA seq data analysis. The error occurred and there was no bam file generated. The error information is listed as follow:

[Thu Jan 11 15:42:04 2018] Inspecting Bowtie index files
[Thu Jan 11 15:42:04 2018] Checking reference sequence length
[Thu Jan 11 15:42:29 2018] Checking consistency of Bowtie index and reference sequence
[Thu Jan 11 15:42:29 2018] Checking read format
[Thu Jan 11 15:44:54 2018] Running MapSplice multi-thread
[Thu Jan 11 17:42:09 2018] Generating junctions from sam file
[Thu Jan 11 17:43:07 2018] Filtering junction by min mis and min lpq
[Thu Jan 11 17:43:07 2018] Filtering junction by ROC argu noncanonical
[Thu Jan 11 17:43:08 2018] Generating synthetic junction sequences
[Thu Jan 11 17:43:27 2018] Checking Bowtie index files
[Thu Jan 11 17:43:27 2018] Building Bowtie index for junction synthetic sequence
[Thu Jan 11 17:43:47 2018] Running MapSplice multi-thread
[Thu Jan 11 20:25:13 2018] Running alignment handler
[MapSplice Running Failed]
Error: filter alignment failed

Is there anyone have encounted this error before? I have read the user guide of MapSplice and couldn't find the solution. I think there may be some problems in filtering unmapped reads but don't know how to solve it. Could you please help me? Thank you very much. Guanghao Li

rna-seq • 68 views
ADD COMMENTlink modified 5 days ago by simo.aufiero0 • written 5 days ago by liguanghaoli0
0
gravatar for simo.aufiero
5 days ago by
European Union
simo.aufiero0 wrote:

Hi Guanghao Li, I had the same problem. I am running mapsplice using the genome reference mm10. I did the analysis in the past by using mm9 and mapsplice pipeline finished without any problem with that genome reference. What genome reference are you using?

Simona

ADD COMMENTlink written 5 days ago by simo.aufiero0

Hi, Simona, I use hg19 as reference. And now I run MapSplice in another computer, the program work well. So I'm also comfused about the error.

ADD REPLYlink modified 3 days ago • written 3 days ago by liguanghaoli0
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