tombo

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Hi ,

I want to resquiggle part of fastq records (because too many of them).

I shuffle fastq record first (to make sure sample evenly) and sample a potion from it, after running resquiggle modue, most sequence do not have resquiggle(Event) group in fast5 file, it is OK, however, if do not shuffle fastq file.

I'm not sure I understand exactly what is the expected behavior and what you are observing. Could you post the exact commands used, the expected output and the observed output?

Hi @marcus1487 , The command I used is

seqkit scat -f ./fq_path | seqkit shuffle | seqkit sample -p 0.1 > sample.fq 

Then I processed as tombo resquiggle instruction and expect dtw result of sampled fastq in correspond fast5 records(in `Events attributes), but if I shuffle sequence order in fastq file, only a potion of sequence have dtw result instead of whole sequence in sample.fq file.

It will not be happened if I use

cat ./*fastq > whole.fq; seqkit sample -p 0.1 whole.fq> sample.fq

The only difference is whether shuffle the order of sequence in fastq file.

Thanks

What are the tombo commands you are using? In order to get fastq results into the FAST5 file you would need to use the preprocessing tombo command. What was the output of this command?

I'm not familiar with seqkit, so I can't help much there.