I need to align several libraries of Ribo-seq reads that are on average 30 nt long to a genome of about 2Gbp. I'm using the following parameters currently,
Indexing:
../hisat2-2.1.0/hisat2-build --ss ss.txt --exon exon.txt genome.fa index_prefix
The overall alignment rates are around 30%-40%. So in order to increase the alignment rate, are there any recommended special parameter values that I should use in generating the index and in running the hisat2 alignment with such short reads?
Hi there,
I need to align several libraries of Ribo-seq reads that are on average 30 nt long to a genome of about 2Gbp. I'm using the following parameters currently, Indexing: ../hisat2-2.1.0/hisat2-build --ss ss.txt --exon exon.txt genome.fa index_prefix
Mapping: ../hisat2-2.1.0/hisat2 \ -x index_prefix \ -k 200 --phred64 --mp 1,1 --score-min L,0,-0.1 \ -U input_1.realclean.fq.gz -S output_riboseq.sam
The overall alignment rates are around 30%-40%. So in order to increase the alignment rate, are there any recommended special parameter values that I should use in generating the index and in running the hisat2 alignment with such short reads?
Thanks for hisat2 and for any suggestion!
Best regards, Zhiyi