User: Bastien Hervé
Bastien Hervé • 2.2k
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- Limoges, CBRS, France
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Posts by Bastien Hervé
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... I don't want to take up any of your time, if you please I need an advise here
I will implement this solution in python using this [pseudocode][1]
But I disagree with the Soft Clip/Hard Clip event :
- Case1 ( M/X/=) :
- start at the specified mapping position, set counter to 1
- Add 1 t ...
written 1 hour ago by
Bastien Hervé • 2.2k
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... Thanks Pierre for this solution and I bet this one is working very well, but I don't want to mess with Java in my python script. ...
written 1 hour ago by
Bastien Hervé • 2.2k
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... My reads are RNA, this read map on the reference from 113260099 to 113260237(113260099+138), then huge gap (169544N), then map from 113429781(113260099+138+169544) to 113429794(113260099+138+169544+13).
The logic is that this read map from 113260099 to 113260237 and from 113429781 to 113429794
My ...
written 16 hours ago by
Bastien Hervé • 2.2k
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... I'm trying to use `samtools view` to get reads falling in a given area
samtools view in.bam 'chr12:113428514-113428567' | grep "NB500938:125:HY3KMBGX3:4:21501:7767:16841"
NB500938:125:HY3KMBGX3:4:21501:7767:16841 99 chr12 113428559 255 151M = 113428600 169 CATAGTAATCACAATAGTGGATTTTTCCTCTATA ...
written 17 hours ago by
Bastien Hervé • 2.2k
• updated
16 hours ago by
Pierre Lindenbaum ♦ 113k
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... You can get all the unique patient id, then :
- Loop over this list
- For each loop take the patient id and subset your GRanges using the patient id (you'll get a sub Granges with the information of the patient with this id)
- Do whatever you want with the sub GRanges ...
written 17 hours ago by
Bastien Hervé • 2.2k
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... Sounds like a school project, could you show what you have tried to get a starting point to work on ? ...
written 22 hours ago by
Bastien Hervé • 2.2k
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... For counting I see no problem to delete the ALT_Loci and Patch sequences
For variant calling :
> Reads will get a very low mapping quality as they can map to the primary assembly and the ALT_Loci. Saying this you are unable to do variant calling for this regions, as reads that can map to multip ...
written 1 day ago by
Bastien Hervé • 2.2k
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... Thanks for the detailed answer ! As I can understand masking PAR region of Y chromosome for variant calling does not lead to false detection.
For counting, using the fact that these regions are similar, if you do not mask PAR region on Y you will have bad alignment on these regions (multi mapping). ...
written 1 day ago by
Bastien Hervé • 2.2k
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... For each patient you can subset the Granges using `Participant` column. Then you have a subGRanges with only the data of your patient that you can work with. ...
written 1 day ago by
Bastien Hervé • 2.2k
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... What is your error ?
Please do your import at the begining of your script `from Bio.Align.Application.import mafftcommandline` ...
written 1 day ago by
Bastien Hervé • 2.2k
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