-
Dear all,
I wanted to use BGLR to estimate the genome-wide variance explained of a trait by SNPs and DNA methylation . A colleague and I noticed that BGLR estimates substantial SNP heritability or …
-
Greetings,
I am trying to run the VCF file of 38,000 variants. The rest of the databases run effiicently but it's taking almost 20-30 minutes in dbnsfp (although the index is generated) annotation.…
-
Hello,
I was not able to run successfully SINE_Scan on a subset of my assembly (for testing purposes).
The command I used was:
`perl SINE_Scan_process.pl -s 123 -g /path/subset.fa -o /path/test_id2…
-
Hi, I wanted to try the phyloligo method on my data but encountered the following error.
I installed it through conda.
I obtain the error when using `--large memmap`.
```
❯ phyloligo.py -i
-
Hi Fang,
Thanks for this great package! I'm stuck at the runHomer function as i need to pass the argument '-preparsedDir' from the findMotifsGenome.pl function but it doesnt seem to work when i add…
-
In many genomes (most plants, for example), there is an abundance of repetitive DNA that is recalcitrant to short read mapping. This means that if I break my genome down into fixed-width windows, I wi…
-
PrimerPooler is supposed to be fast, and part of its speed comes from parallelisation. The Java port is currently not parallelised, so will be slower than the C version (and I'd like users to know if…
ssb22 updated
3 years ago
-
Few issues, some are tool related, but might be global.
**Example tools:** Tophat2 and SAM-to-BAM
**Impact:**
- SAM-to-BAM genome selection can only be done within the editor, manually, without bene…
-
Hi there. I'm attempting to run the selection analyses function with the command:
selectionanalyses(do_meta=FALSE,do_pairwise=TRUE,export='pdf', do_fsthet=FALSE, do_pcadapt=FALSE, do_outflank=FALSE…
-
hello
my reference genome is Ensemble v41 hg38.
but your reference genome is ucsc hg38.
so i changed chromosome annotation according to ucsc chromosome version in my vcf file
(ex) GL383518.1…