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shenkers / isoscm

Transcript assembly tool using multiple change-point inference to improve 3'UTR annotation
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No subgroup and gtf file is created after running the software #23

Open ruixuan-zhang opened 4 years ago

ruixuan-zhang commented 4 years ago

Hi everyone, I met some problems when using this software. I basically follow the guide and my argument are a BAM, a base name, and reverse_forward.

Then, I got this, I think there is nothing wrong with it

2020-10-21T09:26:11,643 [main] INFO  executable.IsoSCM - IsoSCM 2.0.12
2020-10-21T09:26:17,463 [main] INFO  executable.IsoSCM - Command: java -jar  IsoSCM-2.0.12.jar assemble -bam /aptmp/ruixuan/medusavirus_paper/mapping_result/merged_genome/MVPI16/MVPI16_sort.bam -base medusa -s reverse_forward
2020-10-21T09:26:17,484 [main] INFO  executable.IsoSCM - Starting assemble ...
2020-10-21T09:26:17,632 [main] INFO  executable.IsoSCM - tabulating splice junctions...
Exception in thread "main" java.lang.NullPointerException
    at processing.FindSpliceJunctions.tabulateSpliceJunctions(FindSpliceJunctions.java:148)
    at executable.IsoSCM.main(IsoSCM.java:240)

But as a result, I only have 

`
|--- log file
|--- isoscm folder
       |----a XML file 
       |----tmp folder (containing an empty bed file with my base name)

So I'm not sure I got the right output from this software and what should I do to correct it? Thank you

shenkers commented 4 years ago

Hi Richard,

How did you align the reads? IsoSCM expects the reads to have a flag that indicates the strand inferred from the splice junction motifs. I know this flag was added by tophat, but I'm not sure about other tools.

On Tue, Oct 20, 2020, 8:34 PM Richard notifications@github.com wrote:

Hi everyone, I met some problems when using this software. I basically follow the guide and my argument are a BAM, a base name, and reverse_forward.

Then, I got this, I think there is nothing wrong with it

2020-10-21T09:26:11,643 [main] INFO executable.IsoSCM - IsoSCM 2.0.12 2020-10-21T09:26:17,463 [main] INFO executable.IsoSCM - Command: java -jar IsoSCM-2.0.12.jar assemble -bam /aptmp/ruixuan/medusavirus_paper/mapping_result/merged_genome/MVPI16/MVPI16_sort.bam -base medusa -s reverse_forward 2020-10-21T09:26:17,484 [main] INFO executable.IsoSCM - Starting assemble ... 2020-10-21T09:26:17,632 [main] INFO executable.IsoSCM - tabulating splice junctions... Exception in thread "main" java.lang.NullPointerException at processing.FindSpliceJunctions.tabulateSpliceJunctions(FindSpliceJunctions.java:148) at executable.IsoSCM.main(IsoSCM.java:240)

But as a result, I only have

` |--- log file |--- isoscm folder |----a XML file |----tmp folder (containing an empty bed file with my base name)

So I'm not sure I got the right output from this software and what should I do to correct it? Thank you

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francicco commented 1 year ago

Hi I'm having the same problem. I aligned the reads with STAR Cheers F

shenkers commented 1 year ago

Hi @francicco, IsoSCM depends on the aligner setting an XS flag in order to infer the read strandedness. I did a search, and it looks like the author of STAR has actually added a flag for this -outSAMattributes XS (from this GH issue https://github.com/alexdobin/STAR/issues/567 ). Does running STAR with this flag help solve this problem?

shenkers commented 1 year ago

@francicco It looks like iRNA-COSI has made a nextflow workflow for running IsoSCM. They're using STAR for the alignments, and they are adding the XS flag https://github.com/iRNA-COSI/APAeval/blob/main/execution_workflows/IsoSCM/modules/star_alignment.nf