Hi, I am a newbie for NGS, I was experimenting with chip-seq analysis with galaxy-bowtie.
Question is:
what does the XM:i:N mean in the bowtie file? Reason I ask is:
My research shows it means (from bowtie manual) : "For a read with no reported alignments, <N> is 0 if the read had
no alignments. If [-m] was specified and the read's alignments
were supressed because the [-m] ceiling was exceeded, <N> equals
the [-m] ceiling + 1, to indicate that there were at least that
many valid alignments (but all were suppressed). In [-M] mode, if
the alignment was randomly selected because the [-M] ceiling was
exceeded, <N> equals the [-M] ceiling + 1, to indicate that there
were at least that many valid alignments (of which one was reported
at random)."
I've pasted few lines from the bowtie output. I noticed when there is a unique match, the XM:I field is not shown. When XM:i:1 or XM:i:0, there is no match. Problem is shouldn't XM:i:1 mean there is a match????
Here is the bowtie parameters:
ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 6 -S -n 2 -e 70 -l 28 --maxbts 125 -k 1 -m 1 --phred33-quals /galaxy/data/hg19/hg19full/bowtie_index/hg19full /galaxy-repl/main/files/019/148/dataset_19148014.dat"
QNAME FLAG RNAME POS MAPQ CIGAR MRNM MPOS ISIZE SEQ QUAL OPT
SRR4237722.115 HS38_18889:1:1101:10918:1975 length=50 4 * 0 0 * * 0 0 GGGTCNCACTCTGTCACCCAGGCTGGAGTGCAGTGGCCGTGATCTCGGCT BCCDF!2AAFFHHIJJIJIJFHIIDGIGFCEGGHIIJGIDHIIJIEEHHH XM:i:1
SRR4237722.108 HS38_18889:1:1101:10120:1993 length=50 4 * 0 0 * * 0 0 ATTCCATTCCACTCCATTCCATTCCAATCCTTTCCGCTCGGGTTGATTCC CCCFFEFFGHHHGJIJJIIIIIJJJJJJIJJJIJJJJJJJII?FHIIJJJ XM:i:0
SRR4237722.168 0 chr13 75065209 255 50M * 0 0 CACTGGAGCCTCTGATATCTTTTTTCTTTTTCCTGCTGACACAGGACTGC CCCFFFDEHHHHHIIJJJJJJJJJJIJIGGJIJJIIJJJJJIJJJIJIJJ XA:i:0 MD:Z:50 NM:i:0
SRR4237722.94 0 chr3 121413904 255 50M * 0 0 TGATGNAACCGATTCTGAACATGTAGGTCTTGTGCTCATACTCAGAGAGT @@?DD!2=CFHHHFHIIF>GHIIHCGI*@FGHFGIIIIHIIHGIIIGIID XA:i:1 MD:Z:5G44 NM:i:1
I will really appreciate any help.