...
index: STAR genome indices
- bam_output: all sample only bam files in directory
- sample1.Aligned.sortedByCoord.out.bam
- sample1.Aligned.sortedByCoord.out.bam
- output: individual sample
STAR_output: Default output files from STAR which includes
Log.out: main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging.
sample1.Log.progress.out: reports job progress statistics, such as the number of processed reads, % of mapped reads etc.
sample1.Log.final.out: summary mapping statistics after mapping job is complete, very useful for quality control.
sample1.Aligned.out.bam - alignments in standard SAM format.
sample1.SJ.out.tab- only those reads that contain junctions.
- sample1.Unmapped.out.mate1- output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s)
- sample1.Unmapped.out.mate2-output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s)
More information on the tool can be found here - https://github.com/alexdobin/STAR
...