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mcfrith / tandem-genotypes

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Compatibility with faster aligner #4

Closed MaestSi closed 5 years ago

MaestSi commented 5 years ago

Dear tandem-genotypes developers, I would like to know if the tool works only with Last alignment files or if you know of any other aligners that can produce a maf file more quickly. I am asking this since, in my experience, Last is much slower than aligners as minimap2 that, however, seem to work only with paf and sam output formats. Thanks in advance, Simone

satomimitsuhashi commented 5 years ago

Dear Simone I hope this helps... I routinely use LAST for long read human genome data (~100Gb). It finishes alignment process within a day when I use -P16. I found LAST is slightly slower than minimap2 but much faster than ngmlr, if I use masked reference. The method is described here (option 2). https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md I have not found any major problems in using masked reference for tandem-genotypes analysis so far. Satomi

2019/07/27 0:43、Simone Maestri notifications@github.com<mailto:notifications@github.com>のメール:

Dear tandem-genotypes developers, I would like to know if the tool works only with Last alignment files or if you know of any other aligners that can produce a maf file more quickly. I am asking this since, in my experience, Last is much slower than aligners as minimap2 that, however, seem to work only with paf and sam output formats. Thanks in advance, Simone

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MaestSi commented 5 years ago

Thank you for the kind information. Do you know if there is a way for converting maf format to bam format? I used maf-convert for converting maf to sam, but then I had no header, and so I could not compress it to bam. What do you usually do if you want to inspect mapped reads in IGV, for example? Thanks again

satomimitsuhashi commented 5 years ago

I think you just need to add -d option when making sam file, then cover to bam file using samtools like this. maf-convert sam -d file.maf > file.sam samtools view -bS -o file.bam file.sam samtools sort file.bam sorted samtools index file.bam Hope this helps.

2019/07/27 23:59、Simone Maestri notifications@github.com<mailto:notifications@github.com>のメール:

Thank you for the kind information. Do you know if there is a way for converting maf format to bam format? I used maf-convert for converting maf to sam, but then I had no header, and so I could not compress it to bam. What do you usually do if you want to inspect mapped reads in IGV, for example? Thanks again

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MaestSi commented 5 years ago

Dear satomi, thank you so much. I had not understood that 'dictionary of sequence lengths' was something related with the sam header.