Thank you very much
Is there any post/manual/blog to summarize the attribute tag (optional field) of tophat output bam file? How many attribute tags does tophat output bam file have? What is the meaning of each tag?
I run the tophat for HiSeq2000 paired-end 2*100bp strand-specific, with the option --library-type fr-firststrand. The output 13 tags is as below, are there any other tags? Is it right for my understanding?
AS:i: alignment score generated by alignerCC:Z: reference name of the next hit; "=" for the same chromosomeCP:i: leftmost coordinate of the next hitHI:i: query hit index, indicating the alignment record is the i-th one stored in SAMMD:Z: string for mismatching positions.NH:i: number of reported alignments that contains the query in the current record.NM:i: edit distance to the reference, including ambiguous bases but excluding clippingXG:i: the number of gap extensions, for both read and reference gaps, in the alignment.XM:i: the number of mismatches in the alignmentXN:i: the number of ambiguous bases in the reference covering this alignmentXO:i: the number of gap opens, for both read and reference gaps, in the alignment.XS:Z: if either fr-firststrand or fr-secondstrand is specified, every read alignment will have an XS attribute tag as explained below.YT:Z: value ofUUindicates the read was not part of a pair. Value ofCPindicates the read was part of a pair and the pair aligned concordantly. Value ofDPindicates the read was part of a pair and the pair aligned discordantly. Value ofUPindicates the read was part of a pair but the pair failed to aligned either concordantly or discordantly. Filtering: #filtering
The resource I have read: https://ccb.jhu.edu/software/tophat/manual.shtml
The above description of "XS": http://samtools.github.io/hts-specs/SAMv1.pdf
The above description of "AS", "CC", "CP", "HI", "MD", "NH", "NM": http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#bowtie2-build-opt-fields-as
The above description of "XG", "XM", "XN", "XO", "YT": I don't know if the tag has the same meaning in bowtie and tophat output bam.
1 answer
Yes, the X? tags described on the bowtie2 page have the same meaning in tophat2. In reality, those are being produced by bowtie2, since that's what tophat uses.
Log in to answer this question.