Comments (6)
This should be possible via the uncalled convert
command. Currently the only way to compare with the projected guppy alignments is to additionally run uncalled dtw
and write to the same SQL file. I should add the standalone basecaller alignment command, but for now the series of commands would be something like this:
uncalled covert --eventalign-in <file.tsv> ... --sql-out <alns.db>:f5c #f5c is the name of the f5c "track"
uncalled dtw ... --sql-out <alns.db>:unc #compute guppy alignment and perform DTW
uncalled dotplot --sql-in alns.db #visualize f5c, uncalled, and basecaller alignments
This is more work than it should be, and soon I'll push an update which will allow you directly visualize an eventalign file. Stay tuned!
from uncalled.
I think I was unclear in my question. Sorry about that. Some time ago I managed to get f5c eventalign results to correctly be loaded. This is about f5c resquiggle. It is a recent module I added to f5c, to output alignment of the signal to the base called read (where as, eventalign outputs the alignment of signal to reference). The output format is a TSV, but slightly different:
https://hasindu2008.github.io/f5c/docs/output
from uncalled.
Ah yes, sorry I forgot resquiggle refered to aligning to the basecalled reads. That will take some reworking to handle reads not aligning to a common reference, but it does sound useful. I will work on it and let you know when I make progress
from uncalled.
Cool. Also, now are you supporting BAM move tables - is there an example of the steps for that?
from uncalled.
I do support BAM move tables now. You just need to run Guppy with the "--moves_out" and "--align_ref" options, merge the resulting BAM files with samtools, then input the merged bam file to "--bam-in" in the uncalled dtw
command. There is one known issue in that Guppy only outputs moves in primary alignments, so you won't be able to align secondary alignments with this method currently. I will work on a workaround for that
from uncalled.
Primaries are enough for me. But loading takes so much time, are you still accessing the signal data from FAST5 when using this BAM method? Looks like most of the time is spent on IO (this is a promethION dataset on an NFS storage).
from uncalled.
Related Issues (20)
- [QUERY] Can I test UNCALLED to always try and map only 2000 raw samples from FAST5 HOT 1
- Uncalled in ubuntu 16 HOT 3
- Segmentation fault in 'uncalled sim' HOT 3
- Floating point exception HOT 8
- uncalled failed to connect to minknow instance HOT 3
- Running Uncalled using Flongle flow cell HOT 2
- Updated Uncalled and Minknow No Longer Working HOT 4
- Generating sequencing summary from fast5 raw reads HOT 1
- [QUESTION] mapping to reference stringency HOT 1
- Installing UNCALLED4 error HOT 12
- [QUESTION] 10X run-time for reads of 500 raw signals HOT 12
- Computer requirement for UNCALLED HOT 1
- `sim` segmentation error HOT 7
- Installation on Ubuntu (issue with compiler) HOT 5
- Sequenced reads are too short HOT 4
- New release HOT 2
- Remove mux scan windows from Flongle run HOT 1
- Error when trying example HOT 12
- Fast5 file `vbz` problem HOT 2
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from uncalled.