-
Notifications
You must be signed in to change notification settings - Fork 11
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Aligning long reads with STAR (e.g. nanopore) #88
Comments
STAR/source/STARlong --genomeDir /mnt/e/Chemello/Spritz0.0.2/Homo_sapiens.GRCh38.dna.primary_assembly --genomeLoad LoadAndKeep --readFilesIn /mnt/e/Chemello/NanoporeX1/nanopore_exp1-trimmed.fastq --limitBAMsortRAM 88156000000 --outFileNamePrefix /mnt/e/Chemello/NanoporeX1/nanopore_exp1-trimmed --outSAMtype BAM SortedByCoordinate --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMismatchNmax 100 --seedSearchLmax 30 --seedPerReadNmax 100000 --seedPerWindowNmax 100 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 |
I gave this a couple days of work. Some notes on nanopore sequencing data:
Some notes on PacBio:
|
We need to check the average read length, and if it's above 250 or so, we'll need to use
STARlong
.To do this, we need to
make clean
in theSTAR/source
directory, and thenmake STARlong
to makeSTARlong
. This doesn't build unlessSTAR
is all cleaned out.We also need less stringent parameters and more seeds per read.
The text was updated successfully, but these errors were encountered: