Open smoretti opened 3 years ago
Hi
We use Kallisto v0.46.0 on Linux and it works very well. But sometimes for some small size libraries it takes much much longer than expected
Those libraries are small size, mostly single-end and with short reads (about 30-36). So we use a short k-mer index on them: 15.
Here is the list of those libraries
SRX1065256 SRP063008 9823 Sus scrofa ERX167126 ERP001954 9823 Sus scrofa ERX167070 ERP001954 9823 Sus scrofa ERX167059 ERP001954 9823 Sus scrofa SRX084382 SRP007512 10181 Heterocephalus glaber SRX084381 SRP007512 10090 Mus musculus SRX147579 GSE36026 10090 Mus musculus SRX147580 GSE36026 10090 Mus musculus SRX147581 GSE36026 10090 Mus musculus SRX147582 GSE36026 10090 Mus musculus SRX147583 GSE36026 10090 Mus musculus SRX147584 GSE36026 10090 Mus musculus SRX147590 GSE36026 10090 Mus musculus SRX147591 GSE36026 10090 Mus musculus SRX147592 GSE36026 10090 Mus musculus SRX147593 GSE36026 10090 Mus musculus
Do you know what could cause this much longer running time?
Usually we don't see such thing with other short read libraries.
I also have the same question. My paired-end RNA-seq read length is 502, using index of 31 kmer, the quant process takes hours, however for 1502, it only takes minutes. Have you solved this?
Hi
We use Kallisto v0.46.0 on Linux and it works very well. But sometimes for some small size libraries it takes much much longer than expected
Those libraries are small size, mostly single-end and with short reads (about 30-36). So we use a short k-mer index on them: 15.
Here is the list of those libraries
Do you know what could cause this much longer running time?
Usually we don't see such thing with other short read libraries.