Heng Li
Heng Li
Oh, 2bp intron. Smells like a bug. I will have a look later.
Actually it occurs to me that `-J` should be larger than `-F`; otherwise a frameshift ~~will always~~ may be aligned as an intron. You may try to reduce frameshift penalty...
Didn't realize the manpage was that old. Now updated to v0.9.
Do you have a small test data set with which I can reproduce the issue? Thanks.
I will mark this repo deprecated as most of the gfaview functionalities are supported by the asm command of gfatools. You can create an issue at gfatools instead.
Need to update the document. Just briefly for now, the BED file gives: chr, start, end, SRF contig name, and mean percent identity (3.21 = 3.21%). You can ignore the...
I just realized that the UCSC format page does not explicitly require that BED should be TAB delimited. However, the "BED detail format" does require TAB as the only separator....
As is implied by the name of "tabix", the manual page and the paper, tabix only works with TAB-delimited formats. You can convert other delimiter easily with `tr " "...
> My understanding is @lh3 considers minimap2 to make bwa mem obsolete. For long reads, minimap2 should be mostly better than bwa-mem. I wouldn't recommend to use bwa for long...
With fermikit, you would need something like this. ``` sh your_split_script.py ref-concat.fa 100 90 > pseudo-reads.fa # chop to 100bp with 90bp overlap fermi.kit/fermi2.pl unitig -p prefix -El 100 -m0...