tRAX Mismatch Track Hub: Spn_CSP

This track hub description is automatically generated by the program tRAXtracks.py. It contains information on the provided tracks and on the code that created this track hub.

 

Experiment information:

PLEAE UPDATE

 

Available assemblies:

strePneu_TIGR4_ATCCBAA_334
- TIGR4_3hr mismatch
- TIGR4_3hr_+AlkB mismatch
- TIGR4_3hr_+CSP mismatch
- TIGR4_3hr_+CSP_+AlkB mismatch

 

Mismatch tracks:

Mismatch tracks show the fraction of mismatching and deleted bases at each position in the reads aligned to the specific tRNA, overlaid on the coverage value at each position.

Mismatch color key:

 

Actual base

 

A mismatch

 

G mismatch

 

T mismatch

 

C mismatch

 

Deletion

 

Methods and data sources:

Data inputs: samtools mpileup files from aligned sequencing reads, the genome assembly name(s), and the chromosome size file(s) for the assembly downloaded from the UCSC genome browser ftp site.

Calculations and visualization: The abundance of mismatch, reference and deletion characters is averaged across grouped mpileup files. Mismatch, reference and deletion abundance is split into separate bigWig files, then stacked inside a multiWig container.