Help with seqkit sort increasing file size in multifasta
Hi everyone, I need to sort a big multifasta file (around 160GB) using the seqkit sort option and I've noticed that the sorted output is heavier than the input. Does anybody know why could this happen? I've used seqkit sort -N.
Thanks in advance!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Help with treetime ancestral MissingDataError
written by FJCF •
-
Question about seqkit sort function
written by FJCF •
-
Remove reference sequence from multifasta file
written by FJCF •
-
Sorting (big) FASTQ file
written by mathieu.bahin
-
High rate of no_feature in htseq-count despite high alignment rate in hisat2
written by mk.english232 •
-
why bowtie2 doesn’t report longer than 500bp inserts?
written by Dan •
-
bcftools consensus overlapped variant
written by Ak •
-
differential expression in R
written by sam •
-
rMATS BAM file MemoryError Issue
written by saipra003 •
-
Samtools, not sorting a bam file correctly ?
written by pinn
Does the input file contain long sequence lines while the sorted uses fixed width chunks?
I've checked it and both files have a multiline sequence with a fixed size with this structure:
If the width is the same on both files the number of lines should be the same right?
please paste the result of 'seqkit stats' and 'seqkit sum' with the two files.
For questions or bugs of a specific tool, asking the author is also a good way: https://github.com/shenwei356/seqkit/issues
Never use file sizes as a criteria for any QC/comparison other than in a qualitative way. e.g. is a file present. Is it zero bytes or does it contain stuff.
Perhaps this also applies in your case: https://askubuntu.com/questions/796947/why-is-my-sorted-file-bigger