-
Hi,
I have some questions about the tags added to the .bam output file after running `uncalled4 align`. I would like to write a custom script, that reads the alignments from the uncalled4 .bam file…
-
Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
```
# extract consensus sequences from profiles
…
-
In https://github.com/TGAC/KAT/issues/94#issuecomment-385328131 I mentioned an issue with directly calling:
```
$ for f in pe_vs_assembly-main.mx pe_vs_assembly-ends.mx pe_vs_assembly-mixed.mx pe_…
-
See https://github.com/dib-lab/kevlar/issues/31.
Accumulate hashed k-mers in some kind of buffer1. The first time the buffer reaches a user-specified size, go through each band one-by-one, create a…
-
synopsis: When running FastK with -k set 32 or less, I'm seeing segfaults.
Specifically, I've seen this with one particular input file (the blue whale assembly) and k in {20,26,31,32}.
Details:
…
-
David Koslicki convinced me this was a good idea.
-
When clustering or searching with short sequences, obvious hits may be missed. This is also a problem when much of the sequences are masked. It is probably due to few distinct unmasked k-mers in the s…
-
I download the transcriptome fasta from uscs, https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/mrna.fa.gz . when I used kallisto index to bulid the index for kallisto, that had two warning:
…
-
I have an application where I need to count pairs of k-mers separated by a fixed distance. This is almost identical to K-mer counting where K=2k, the "only" change should be in the scanning step where…
-
Hey Rayan,
I was exploring some compressed logan runs and noticed a significant loss of k-mers when comparing unitigs/contigs to the full read content in the SRA. Are you applying a filter to exclu…