User: colindaven

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colindaven1.6k
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Posts by colindaven

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Comment: C: Placing SNPs within updated genome assembly
... 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 colindaven1.6k
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Comment: C: BioNano fasta file formatting issue
... 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 colindaven1.6k
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Answer: A: How to evaluate sequence alignment (e.g. number of indels) of ONT data after dat
... - 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 colindaven1.6k
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Answer: A: How to Analyze Overlapping Peaks using ChIP-Seq Data
... 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 colindaven1.6k
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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 colindaven1.6k
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Answer: A: MaSuRCA error: can't find 'gatekeeper' program
... 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 colindaven1.6k
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Answer: A: Filter nanopore fastq files by start time
... 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 colindaven1.6k
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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 colindaven1.6k
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Answer: A: Best Genome Assembler and Genome Annotation tools and pipelines
... 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 colindaven1.6k
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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 colindaven1.6k

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