Hi all
I'm really nub to working with bowtie. I have two fq files that contained paired end reads for a child . The files are child1-1.fq and child1-2.fq and I have a reference file with the name of ref.fa . I want use bowtie to map this paired end read to the reference seq and I'm using the following command but the output wasn't good. I think that I don't use correct option like -I and -X . actually I don't what should I select for those options .
any suggestion will be nice.
thanks you all.
my command is:
and the output is :
some lines of child1-1.fq:
and some lines of child1-2.fq:
I'm really nub to working with bowtie. I have two fq files that contained paired end reads for a child . The files are child1-1.fq and child1-2.fq and I have a reference file with the name of ref.fa . I want use bowtie to map this paired end read to the reference seq and I'm using the following command but the output wasn't good. I think that I don't use correct option like -I and -X . actually I don't what should I select for those options .
any suggestion will be nice.
thanks you all.
my command is:
Code:
bowtie-build ref.fa ref_index bowtie -v 2 -S ref_index -1 child1-1.fq -2 child1-2.fq > child1_align.sam
Code:
# reads processed: 25000 # reads with at least one reported alignment: 16 (0.06%) # reads that failed to align: 24984 (99.94%) Reported 16 paired-end alignments to 1 output stream(s)
@child_1192360_1192917_1:0:0_1:0:0_2dc6c/1
GGACTTTGAGCTCGGGATGAATGTGCCTGCTGACTTTGCTGTTGCCTCTGTTGTAATCTATTATTCACTG
+
2222222222222222222222222222222222222222222222222222222222222222222222
@child_652211_652627_0:0:0_2:0:0_2dc6d/1
TTTTTATGAGCTCATGTTATAAATACAGATAAGACAGAATTGAGAACGAGGAGAAAGAGCGATCTATGCG
+
2222222222222222222222222222222222222222222222222222222222222222222222
GGACTTTGAGCTCGGGATGAATGTGCCTGCTGACTTTGCTGTTGCCTCTGTTGTAATCTATTATTCACTG
+
2222222222222222222222222222222222222222222222222222222222222222222222
@child_652211_652627_0:0:0_2:0:0_2dc6d/1
TTTTTATGAGCTCATGTTATAAATACAGATAAGACAGAATTGAGAACGAGGAGAAAGAGCGATCTATGCG
+
2222222222222222222222222222222222222222222222222222222222222222222222
@child_1192360_1192917_1:0:0_1:0:0_2dc6c/2
GGAACTGGTCAAAAATATTAACACATATGGCTACACTTGGGAATTGATTAGTGCACATATGACACATCGC
+
2222222222222222222222222222222222222222222222222222222222222222222222
@child_652211_652627_0:0:0_2:0:0_2dc6d/2
ACTAAGATTTCATTCCAACACTACATTTTTTCGGAAAACGTTTTATTGAAGTACTGCTTTATGGTCAGCA
+
2222222222222222222222222222222222222222222222222222222222222222222222
GGAACTGGTCAAAAATATTAACACATATGGCTACACTTGGGAATTGATTAGTGCACATATGACACATCGC
+
2222222222222222222222222222222222222222222222222222222222222222222222
@child_652211_652627_0:0:0_2:0:0_2dc6d/2
ACTAAGATTTCATTCCAACACTACATTTTTTCGGAAAACGTTTTATTGAAGTACTGCTTTATGGTCAGCA
+
2222222222222222222222222222222222222222222222222222222222222222222222
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