User: mehmetgoktay1989

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Posts by mehmetgoktay1989

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Running Pindel individually per sample rather than running everything as it expects
... Hi Everyone, I would like to identify SVs including indels, deletions, tandem duplications and inversions. I have tried to run samples first individually and then all of them at once. (lets say 3-4 samples). It definitely gives different results for these two approaches. Is there anyone who can ...
ngs svs pindel written 5 months ago by mehmetgoktay19890
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Comment: A: PacBio: Subread Extraction with bash5tools.py
... Looks like SMRTbell adapter sequences were removed by the program. Thank you! ...
written 12 months ago by mehmetgoktay19890
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PacBio: Subread Extraction with bash5tools.py
... Hi Everyone, I need to convert .h5 files to fasta/fastq files and need to filter based on subread length and quality score. I have installed bash5tools.py and I was able to do what I wanted. But I am a bit confused. After converting .h5 files to fastq and applying filtering. Do I still need to r ...
assembly pac-bio written 12 months ago by mehmetgoktay19890
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Answer: A: Pacbio: extract fastq from h5 file based on quality filtering
... Could you please tell me If bash5tools.py also removes adapter sequences? I have just used it and got subreads from raw data but I am not sure whether subreads still contains adapter sequences? ...
written 12 months ago by mehmetgoktay19890

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