Hi,
I used bowtie to align exome sequencing (Illumina GA), and this is what I got:
# reads processed: 37205349
# reads with at least one reported alignment: 141065 (0.38%)
# reads that failed to align: 37064284 (99.62%)
Reported 141065 alignments to 1 output stream(s)
I am wondering what went wrong.
By the way, here is the .fastq file looks like,
@SRR350953.3 MENDEL_0047_FC62MN8AAXX:1:1:1488:946 length=152TTTTTTTT
NTCCCATTATCTCAAGCAGCCATATGTTTCTCATTCACTTGATACACTGTTTCTTTTCAACCCCCACATCCTCACCGTGCTCAA
ACAAAGAAACAGGTGGTGAGGATGTGGGGGTTGAAAAGAAACAGTGTATCAAGTGAATGAGAAACATA########B@<7:EFE
+SRR350953.3 MENDEL_0047_FC62MN8AAXX:1:1:1488:946 length=152EEB@@>>D
############################################################################FAD=FCCC
CCFDD;E??@@FD?BD>F?FB=BFAEFDGGDGGDG@BB=5=/;?8B=DDDGDGBDGDACAE@B@G88;CTCCTTCCAGGACCCA
Thanks!
I used bowtie to align exome sequencing (Illumina GA), and this is what I got:
# reads processed: 37205349
# reads with at least one reported alignment: 141065 (0.38%)
# reads that failed to align: 37064284 (99.62%)
Reported 141065 alignments to 1 output stream(s)
I am wondering what went wrong.
By the way, here is the .fastq file looks like,
@SRR350953.3 MENDEL_0047_FC62MN8AAXX:1:1:1488:946 length=152TTTTTTTT
NTCCCATTATCTCAAGCAGCCATATGTTTCTCATTCACTTGATACACTGTTTCTTTTCAACCCCCACATCCTCACCGTGCTCAA
ACAAAGAAACAGGTGGTGAGGATGTGGGGGTTGAAAAGAAACAGTGTATCAAGTGAATGAGAAACATA########B@<7:EFE
+SRR350953.3 MENDEL_0047_FC62MN8AAXX:1:1:1488:946 length=152EEB@@>>D
############################################################################FAD=FCCC
CCFDD;E??@@FD?BD>F?FB=BFAEFDGGDGGDG@BB=5=/;?8B=DDDGDGBDGDACAE@B@G88;CTCCTTCCAGGACCCA
Thanks!
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