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friend1ws / nanomonsv

SV detection tool for nanopore sequence reads
GNU General Public License v3.0
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TypeError: NoneType object is not subscriptable, if cigarstring == * #22

Closed Simarpreet-Kaur-Bhurji closed 1 year ago

Simarpreet-Kaur-Bhurji commented 2 years ago

Hi team, I was using Nanomonsv to compare control vs tumor sample. I know this tool is made for long reads, but I currently only have long reads for tumor sample and short reads for the control samples. The Nanomonsv parse works perfectly for the long read tumor sample but throws the following error for the control sample: TypeError: 'NoneType' object is not subscriptable (at parse.py line 44) My understanding of the error is that, if the cigarstring == *, the code is not able to handle it. Can you please look into it?

friend1ws commented 2 years ago

Thank you very much for the report. First, I do not recommend using nanomonsv with mixed tumor and control data. But, If you send me the small BAM control files, then I will look into them.

Simarpreet-Kaur-Bhurji commented 2 years ago

Hi Yuichi, Thank you for getting back to me. But I have used pysam to get rid of the alignments where the cigarstring == * and was able to go through the Nanomonsv pipeline successfully. However, I was wondering if you have any recommendations for structural variation visualisation tools for the results obtained from naomonsv?

Regards, Simarpreet

On Tue, Jun 14, 2022 at 12:37 AM Yuichi Shiraishi @.***> wrote:

Thank you very much for the report. First, I do not recommend using nanomonsv with mixed tumor and control data. But, If you send me the small BAM control files, then I will look into them.

— Reply to this email directly, view it on GitHub https://github.com/friend1ws/nanomonsv/issues/22#issuecomment-1154005517, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ6TYFORNXBGOW233V5ZGCLVO5BS3ANCNFSM5XW6Q44Q . You are receiving this because you authored the thread.Message ID: @.***>

friend1ws commented 1 year ago

Sorry for the late reply. I recommend using IGV or Jbrowse2, to see the BAM file. For interpretation of SVs such as MEI, I'm still wondering which is the best way..