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Old 08-22-2019, 01:34 AM   #241
GenoMax
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@darthsequencer: You can use kmercountexact.sh from BBMap suite.
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Old 03-10-2020, 01:05 AM   #242
roselaw27
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Default Trouble parsing header

Dear BBMap team:

I tried to use filterbytile.sh to remove the reads with low quality, but I encountered an error message saying that there was a trouble parsing the header. I've read the description of the script and Brian Bushnell said that was possible when the reads were renamed (such as in SRA) and to contact him if such error happened.

I downloaded the sequencing data (SRA) from ncbi and used fastq-dump to get the fastq files. I wonder if there is a solution to this?

Thank you very much!
Rose
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Old 03-10-2020, 04:13 AM   #243
GenoMax
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@roselaw27: You can use `-F` option with fastq-dump to try and recreate fastq headers in original illumina format.
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Old 03-10-2020, 05:23 PM   #244
roselaw27
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Thank you for your respond. Unfortunately I tried using -F and filterbytile.sh still showed the same error message. The data were from HiSeq 2500.

Thank you again. I think I am going to try to find other ways to solve the problem.

Rose
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Old 04-03-2020, 08:40 AM   #245
AndrewP
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I'm trying to use BBmap to find all perfect hits or hits with an indel length 1.


Code:
bbmapskinner.sh  in=kmer.fasta out=result.sam ambiguous=all strictmaxindel=1
I'm running a control experiment where I have a subsequence to a larger sequence in the reference. I can find the subsequence in the reference if it's an exact match. However, if I add an indel in either the subsequence or reference, BBmap is unable to map the reference. I thought by setting strictmaxindel to 1, it should be able to report an alignment with a single indel. I've tried setting strictmaxindel to 10 and it still doesn't find the alignment.

Is there something that I am doing wrong?
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