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Old 08-22-2012, 05:03 AM   #1
Location: USA

Join Date: Jun 2012
Posts: 23
Default SeqTrimMap mapping issue

I have Illumina smallRNA-RNAseq reads that have already had their adapters removed and have been filtered for tRNA/rRNA.

I'm trying to use SeqTrimMap to align these reads to my reference genome with the following command:

$SeqTrimMap -b -S -i -v 1 -o ~/seqtrimmap_B_output_496_1 -s -u 18 -t 28 ~/496_1_filtered_18_28nt.fa  ~/zma_b.fa
The program runs well and gives me output in SAM format as requested, but the program will only map reads at lengths 20-24 nt. Does anyone have a suggestion that might allow me to map reads at additional lengths?
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