I tried the following command to map the attached fq file (single end, ChIP-seq).
bowtie -C -p $threads -n 3 -e 160 -a -m 1 --best --strata $BOWTIE2_INDEX/hg19_c s_6.fq -S s_6n.sam 2>&1 | tee s_6n.log
The mappable reads are of only 35%.
# reads processed: 2500
# reads with at least one reported alignment: 885 (35.40%)
# reads that failed to align: 1376 (55.04%)
# reads with alignments suppressed due to -m: 239 (9.56%)
Reported 885 alignments to 1 output stream(s)
The following command gives 38% (as -e is large)
bowtie -p 8 -C -m 10 -l 27 -n 3 -e 950 -k 1 $BOWTIE_INDEX/hg19_c s_6.fq -S s_6.sam 2>&1 | tee s_6.log
# reads processed: 2500
# reads with at least one reported alignment: 972 (38.88%)
# reads that failed to align: 1275 (51.00%)
# reads with alignments suppressed due to -m: 253 (10.12%)
Reported 972 alignments to 1 output stream(s)
But supposedly, SOLiD pipeline should be able map this file for over 50%. Does anybody know how good bowtie is to map SOLiD files? Are there any other parameters that can improve the results?
I see that people said, bfast is better than bowtie for default parameters. By tuning the parameter, can the results of bowtie be improved? Thanks!
http://seqanswers.com/forums/showpos...28&postcount=3
bowtie -C -p $threads -n 3 -e 160 -a -m 1 --best --strata $BOWTIE2_INDEX/hg19_c s_6.fq -S s_6n.sam 2>&1 | tee s_6n.log
The mappable reads are of only 35%.
# reads processed: 2500
# reads with at least one reported alignment: 885 (35.40%)
# reads that failed to align: 1376 (55.04%)
# reads with alignments suppressed due to -m: 239 (9.56%)
Reported 885 alignments to 1 output stream(s)
The following command gives 38% (as -e is large)
bowtie -p 8 -C -m 10 -l 27 -n 3 -e 950 -k 1 $BOWTIE_INDEX/hg19_c s_6.fq -S s_6.sam 2>&1 | tee s_6.log
# reads processed: 2500
# reads with at least one reported alignment: 972 (38.88%)
# reads that failed to align: 1275 (51.00%)
# reads with alignments suppressed due to -m: 253 (10.12%)
Reported 972 alignments to 1 output stream(s)
But supposedly, SOLiD pipeline should be able map this file for over 50%. Does anybody know how good bowtie is to map SOLiD files? Are there any other parameters that can improve the results?
I see that people said, bfast is better than bowtie for default parameters. By tuning the parameter, can the results of bowtie be improved? Thanks!
http://seqanswers.com/forums/showpos...28&postcount=3
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