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No output and "stoi" error with haplotagging data. #5
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I just found out the error disappears if I just process one chromosome. But that would lead to no SV detected with LEVIATHAN. |
Hi, I guess the problem comes from the BX tag in your bam. LRez may not recognize that it is the Haplotagging technology since the BX tag ends with "-1", instead it assumes it is 10X genomics technology and expects the barcode to be a ACGT word. Claire |
Hi clemaitre, I aligned the reads to ref using EMA. To do this, I manually convert haplotagging barcods to 16 bp sequences and did mapping. After that, I reverted the BX tag in bam files back to haplotagging barcodes. So the "-1" comes from the EMA mapper. Thank you . |
Thank you @ZuyaoLiu for these helpful details. Could you give us access to your problematic bam file to help us debugging ? (you can send a download link for instance at claire[dot]lemaitre[at]inria[dot]fr) Claire |
Hi @ZuyaoLiu, the stoi error you got with LRez was fixed, you should now be able to index your bam files using the latest commits (and the "-1" at the end of the barcodes should no longer be a problem neither). The stoi error was due to some contigs whose size is smaller than the windowSize (windowing is used in LRez to multi-thread the indexation). A similar piece of code was also present in LEVIATHAN (which also uses windowing but for SV discovery, thus with a potential similar bug if contigSize<windowSize). This has also been fixed in the latest commit of Leviathan. Could you please test on your data and tell us if it runs without error ? Best, |
Hi Claire,
I just tested with the bam files, and it worked. Thanks for your help!
Best,
Zuyao
Claire Lemaitre ***@***.***> 于2022年3月28日周一 18:03写道:
… Hi @ZuyaoLiu <https://github.com/ZuyaoLiu>,
the stoi error you got with LRez was fixed, you should now be able to
index your bam files using the latest commits (and the "-1" at the end of
the barcodes should no longer be a problem neither). The stoi error was due
to some contigs whose size is smaller than the windowSize (windowing is
used in LRez to multi-thread the indexation).
A similar piece of code was also present in LEVIATHAN (which also uses
windowing but for SV discovery, thus with a potential similar bug if
contigSize<windowSize). This has also been fixed in the latest commit of
Leviathan. Could you please test on your data and tell us if it runs
without error ?
Best,
Claire
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Hi Pierre,
I'm using haplotagging data with LRez and LEVIATHAN.
![微信截图_20220317173942](https://user-images.githubusercontent.com/49354864/158850119-eebc78db-8b9f-4e78-b4fc-18070f13b58c.png)
![微信截图_20220317174118](https://user-images.githubusercontent.com/49354864/158850340-693a7486-ab34-47c9-a34c-a0e0200db524.png)
However, I always got this error when trying to index bam files.
The bam file looks like this:
Any idea about it?
Thank you !!
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