marekkokot
commented
6 years ago Hi, thanks for using KMC. KMC do not support empty reads (are empty reads even allowed in fastq format?). The behaviour you mentioned is a result of KMC's assumption that each read will contain at least one character. Nevertheless, as it seems it may be useful to support them, so I added this functionality with 3284302251236d83153581f87b1cb752ed73c622. Could you please, check if it works for your input? Thanks again for using our software.
Hello,
I'm using KMC to count kmers in fastq files of Illumina paired-end reads. I am using Cutadapt to first trim adapters and low-quality bases, and depending on the read-filtering options I use, the resulting fastq files can have empty reads or not. If I run KMC on a file containing empty reads, it doesn't appear to count the kmers in all of the reads. The command I run is: kmc -k21 -cs1000 -t32 trimmed_R1.fastq kmc_R1 ./kmc_temp/. Below are some output stats.
KMC run on file containing 28114420 reads, including 6222 empty reads Stats: No. of k-mers below min. threshold : 86711467 No. of k-mers above max. threshold : 0 No. of unique k-mers : 122153453 No. of unique counted k-mers : 35441986 Total no. of k-mers : 1505089500 Total no. of reads : 11822644 Total no. of super-k-mers : 222084259
KMC run on file containing 28099409 reads (no empty reads) Stats: No. of k-mers below min. threshold : 199380233 No. of k-mers above max. threshold : 0 No. of unique k-mers : 243868805 No. of unique counted k-mers : 44488572 Total no. of k-mers : 3575041753 Total no. of reads : 28099409 Total no. of super-k-mers : 527520008
Occasionally, running KMC on a file with empty reads gives me a "Wrong input file" error, which is corrected if I remove the empty reads.
What is KMC's behavior when it encounters an empty read? Why does it only count ~40% of the reads, despite only a very small number being empty?
Thank you, and please let me know if you need more information to investigate this.