MAQ easyrun problem and questions.

[answersseq]

Hello guys, your input are much appreciated.
I am running small RNA sequencing here and trying to compare MAQ and the Flicker from illumina.

1. I start with the s_1_sequence.txt file before the adaptor removal. I think Illumina updated their adaptor for small RNA somewhere last year. Should I better use the reads file after adaptor removal?

2. MAQ easyrun worked for me aligning s_1_sequence.txt (renamed to Test_sequence) to the mRNA ref from UCSC (~3.4% aligned). Now, when I tried to align it to mm9.fasta, some error returned. Dose someone have similar experience? (could that because of my laptop's memory is just smaller than ~2.5GB mm9.fa?)

Lenovo:~/maq/maq-0.7.1$ maq.pl easyrun -d TestMm9 mm9.fasta Test_sequence.fastq
-- CMD: /home/Lenovo/maq/maq-0.7.1/maq fasta2bfa /home/Lenovo/maq/maq-0.7.1/mm9.fasta TestMm9/ref.bfa 2> /dev/null
** fail to run command '/home/Lenovo/maq/maq-0.7.1/maq fasta2bfa /home/Lenovo/maq/maq-0.7.1/mm9.fasta TestMm9/ref.bfa 2> /dev/null' at /home/Lenovo/bin/maq.pl line 842.

3. Could you suggest some simple aligner to just align the reads to known miR (or other noncod) database? MAQ seems not working if the reference length is smaller than the reads.

Thanks in advance!