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Forum: Oxford Nanopore 09-19-2017, 06:16 AM
Replies: 4
Views: 3,540
Posted By anotherSAM
Nanopolish 1D

I am working on 1D minion data, albacore 2.0 called, and attempting to use nanopolish on canu derived contigs.
I am trying to follow the github/readme files but find it hard.
...
Forum: Pacific Biosciences 09-07-2017, 07:15 AM
Replies: 14
Views: 5,521
Posted By anotherSAM
I will most likely substitute the quality scores,...

I will most likely substitute the quality scores, but how are they written in PacBio data.
But it is coded scores in fastq so 30 corresponds to something like >
This should work. It will mean canu...
Forum: Pacific Biosciences 09-07-2017, 06:43 AM
Replies: 14
Views: 5,521
Posted By anotherSAM
Genomax, I managed to get the bam2fastx tools...

Genomax, I managed to get the bam2fastx tools working but they provided the same information as samtools and bamtools.
But as we have come to understand this is of no fault of the tools and is...
Forum: Pacific Biosciences 09-07-2017, 04:42 AM
Replies: 14
Views: 5,521
Posted By anotherSAM
head -n1 test.sam ...

head -n1 test.sam ...
Forum: Pacific Biosciences 09-06-2017, 06:42 AM
Replies: 14
Views: 5,521
Posted By anotherSAM
PacBio raw .bam file

I have just received data from my first PacBio sequencing operation and was unaware that the new output format was in .bam file for raw reads, as they are calling the 'better fastq'.
I am using a...
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