Open grantn5 opened 1 month ago
I think this be a raw fastq and it may be correct to perform the following steps for each sample. For instance,
kmc -ci1 -cs10000 -k25 -t${thread} sample1.fq sample1.kmc_db kmc_tmp
kmc -ci1 -cs10000 -k25 -t${thread} sample2.fq sample2.kmc_db kmc_tmp
kmc_tools -t${thread} filter -hm sample1.kmc_db sample1.fq -ci${lower_threshold} sample1._filtered.fq
kmc_tools -t${thread} filter -hm sample2.kmc_db sample2.fq -ci${lower_threshold} sample2._filtered.fq
then construct compacted DBGS for multiple samples:
Bifrost build -c -i -d -k 25 -v -r sample1_filtered.fq -r sample2_filtered.fq -r ... -o cdbg -t ${thread}
Hi thanks for the clarification on the raw vs aligned.
However paired-end sequencing is 2 files from the same sample, one on the forward strand and the other on the reverse strand. How should these be processed with kmc
and subsequently PloidyFrost
?
Sorry for the confusion in my earlier example, files from paired-end reads will be presented as follows
sample1_1.fq
, sample1_2.fq
where both files are from the same sample. One file is the forward strand, and the other is the reverse strand.
Hi Thanks for developing a great tool!
I would just like some clarification on the input to the tool, specifically the
sample.fq
inkmc -ci1 -cs10000 -k25 -t${thread} sample.fq kmc_db kmc_tmp
Should this be a raw fastq or an aligned fastq? Additionally, if it is raw how do you pass paired end reads to the tool?
e.g
sample1.fq
andsample2.fq
Thanks in advance for your help.