Question: is there a post to summarize the attribute tag (optional field) of tophat output bam file?
0
gravatar for zju.whw
4.2 years ago by
zju.whw40
China
zju.whw40 wrote:

Is there amy post/manual/blog to summarize the attribute tag (optional field) of tophat output bam file? Hom many attribute tag does tophat output bam file have? What is the meanning 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, is 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.

 

 

ADD COMMENTlink modified 4.2 years ago by Devon Ryan91k • written 4.2 years ago by zju.whw40
2
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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.

ADD COMMENTlink written 4.2 years ago by Devon Ryan91k

Thank you very much

ADD REPLYlink written 4.2 years ago by zju.whw40
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