is there a post to summarize the attribute tag (optional field) of tophat output bam file?

Question

[zju.whw]

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 aligner
• CC:Z: reference name of the next hit; "=" for the same chromosome
• CP:i: leftmost coordinate of the next hit
• HI:i: query hit index, indicating the alignment record is the i-th one stored in SAM
• MD: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 clipping
• XG:i: the number of gap extensions, for both read and reference gaps, in the alignment.
• XM:i: the number of mismatches in the alignment
• XN:i: the number of ambiguous bases in the reference covering this alignment
• XO: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 of UU indicates the read was not part of a pair. Value of CP indicates the read was part of a pair and the pair aligned concordantly. Value of DP indicates the read was part of a pair and the pair aligned discordantly. Value of UP indicates 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.

Answer 1

[Devon Ryan]

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.

[zju.whw]

Thank you very much