Dear all,
I tried Maq recently on some RNA-seq short read data. I kept getting none of the reads mapped.
Here is my code:
maq fasta2bfa chr1.fa chr1.bfa
maq fastq2bfq Control-6S.HWI-E4_8_3003J.fastq Control-6S.HWI-E4_8_3003J.bfq
#so far so good
maq match Control-6S.HWI-E4_8_3003J.map chr1.bfa Control-6S.HWI-E4_8_3003J.bfq
output for the last line:
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
ras:SRA002355 luow$ head -n 20 nohup.out
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
[match_search] 1% processed in 271.364 sec: 0 / 0 = 0.000
...(output truncated)
[match_search] 99% processed in 573.003 sec: 0 / 0 = 0.000
[match_search] 100% processed in 573.304 sec: 0 / 0 = 0.000
[match_core] sorting the hits and dumping the results...
[ma_load_reads] loading reads...
[ma_load_reads] 24347196*2 reads loaded.
[mapping_count_single] 0, 0, 0, 0
[maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
[match_data2mapping] 0 out of 48694392 raw reads are mapped with 0 in pairs.
-- (total, isPE, mapped, paired) = (24347196, 0, 0, 0)
If you are interested in trying this out, the raw short read data (you may want to use only part of the data for a quick trial) and reference genome can be downloaded by typing:
curl -O ftp://hgdownload.cse.ucsc.edu/golden...ps/chromFa.zip
curl -O ftp://ftp.ncbi.nlm.nih.gov/sra/stati...3003J.fastq.gz
I got similar results when I used ‘maq.pl easyrun’. align reported similar results before here: http://seqanswers.com/forums/showthread.php?t=902, but no soluatoin has been posted. I used a Mac OSX 10.5 system, Maq built from the platform independent version maq-0.7.1.tar.bz2. Any suggestions/thoughts would be greatly appreciated.
I tried Maq recently on some RNA-seq short read data. I kept getting none of the reads mapped.
Here is my code:
maq fasta2bfa chr1.fa chr1.bfa
maq fastq2bfq Control-6S.HWI-E4_8_3003J.fastq Control-6S.HWI-E4_8_3003J.bfq
#so far so good
maq match Control-6S.HWI-E4_8_3003J.map chr1.bfa Control-6S.HWI-E4_8_3003J.bfq
output for the last line:
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
ras:SRA002355 luow$ head -n 20 nohup.out
-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 32.
[ma_load_reads] 24347196*2 reads loaded.
[ma_longread2read] encoding reads... 48694392 sequences processed.
[ma_match] set the minimum insert size as 33.
[match_core] Total length of the reference: 247249719
[match_core] round 1/3...
[match_core] making index...
[match_search] 0% processed in 271.061 sec: 0 / 0 = 0.000
[match_search] 1% processed in 271.364 sec: 0 / 0 = 0.000
...(output truncated)
[match_search] 99% processed in 573.003 sec: 0 / 0 = 0.000
[match_search] 100% processed in 573.304 sec: 0 / 0 = 0.000
[match_core] sorting the hits and dumping the results...
[ma_load_reads] loading reads...
[ma_load_reads] 24347196*2 reads loaded.
[mapping_count_single] 0, 0, 0, 0
[maq_indel_pe] the indel detector only works with short-insert mate-pair reads.
[match_data2mapping] 0 out of 48694392 raw reads are mapped with 0 in pairs.
-- (total, isPE, mapped, paired) = (24347196, 0, 0, 0)
If you are interested in trying this out, the raw short read data (you may want to use only part of the data for a quick trial) and reference genome can be downloaded by typing:
curl -O ftp://hgdownload.cse.ucsc.edu/golden...ps/chromFa.zip
curl -O ftp://ftp.ncbi.nlm.nih.gov/sra/stati...3003J.fastq.gz
I got similar results when I used ‘maq.pl easyrun’. align reported similar results before here: http://seqanswers.com/forums/showthread.php?t=902, but no soluatoin has been posted. I used a Mac OSX 10.5 system, Maq built from the platform independent version maq-0.7.1.tar.bz2. Any suggestions/thoughts would be greatly appreciated.
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