User: colindaven
colindaven • 1.6k
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Posts by colindaven
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... bwa-sw is another tried and tested option for a SNP remapping approach. Warning - remapping SNVs and their flanks is a lossy procedure.
I have I believe read a couple of papers suggesting only a complete remapping of reads will lead to the desired result. Is there some reason you can't do this ? SN ...
written 2 hours ago by
colindaven • 1.6k
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... Looks like it has issues with the lower case bases ? Or the ")" at the end ? Perhaps try redownloading ? Also biopython read fasta and then write fasta methods work well for removing nasty FASTA issues if you can write python, I used to use it all the time.
Can post a script next week if you like ? ...
written 5 hours ago by
colindaven • 1.6k
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... - qualimap might not be modified and appropriate for ONT data
- If you want to easily correct the ONT reads do an assembly with Canu, it will output corrected reads as part of the assembly process if all goes well
- 97% is already a great alignment rate
- mummer is good but does not deliver SAM ...
written 6 hours ago by
colindaven • 1.6k
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... If you have a TSS or alternative epigenomics annotation file of interest (eg from modENCODE) in BED format you can use Bedtools or Bedops to intersect overlapping peaks. ...
written 6 hours ago by
colindaven • 1.6k
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Comment:
C: Processing Raw Nanopore Data
... Try :
guppy_basecaller --print_workflows
I get a lot of different workflows. Eg.
# high accuracy
FLO-FLG001 SQK-LSK108 dna_r9.4.1_450bps_hac
#fast (I believe)
FLO-MIN107 SQK-RAB204 included dna_r9.5_450bps
In my SLURM script I have the following:
ech ...
written 5 days ago by
colindaven • 1.6k
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... Looks like masurca is now available via bioconda. This might save you some time and trouble if you still have issues.
https://anaconda.org/bioconda/masurca
...
written 6 days ago by
colindaven • 1.6k
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... You might try a grep and include the following three lines (as FASTQ contains four lines per read.
So if you want data from 1600-1659 try
`grep -A3 "2019-03-11T16" x.fastq > test.fastq`
Then to see how many reads you filtered out
`wc -l x.fastq`
`wc -l test.fastq`
Check the format is ok too ...
written 6 days ago by
colindaven • 1.6k
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Comment:
C: Processing Raw Nanopore Data
... Yep, I do high accuracy mode calling on a slurm cluster since I don't have a GPU which will work with Guppy. It takes 6-7 times as long as the fast mode calling. We need a GPU and or Minit, if you massively split the input it is quite quick on a cluster too. ...
written 6 days ago by
colindaven • 1.6k
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... There is no "best" assembler for all datasets. I would recommend Soap2denovo to start with. Abyss is also good though produced shorter but highly accurate contigs in my experience. Allpaths LG requires particular data I believe, so I haven't used it.
Two comments:
- the mate-pairs are critical t ...
written 6 days ago by
colindaven • 1.6k
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180
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Comment:
C: >99% unmapped reads
... Good point, could be contamination. You can paste 100 reads into the NCBI blast or a local blast to get a quick impression too. ...
written 8 days ago by
colindaven • 1.6k
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