remote utilities viewer screen not aligning

As an example, a good quality sample will have at least 75% of the reads uniquely mapped.From this file the most informative statistics include the mapping rate and the number of multimappers. Additionally, we get details on splicing, insertion and deletion. The log file provides information on reads that 1) mapped uniquely, 2) reads that mapped to mutliple locations and 3) reads that are unmapped.

We’ll use the less command which allows us to scroll through it easily: One of the output files from the STAR aligner contains mapping statistics, let’s take a closer look at one of those files. Rather than looking at each read alignment, it can be more useful to evaluate statistics that give a general overview for the sample. Having completed the alignment, the first thing we want to know is how well did our reads align to the reference.

Only junctions supported by uniquely mapping reads are reported

SJ.out.tab - high confidence collapsed splice junctions in tab-delimited format.

- job progress with the number of processed reads, % of mapped reads etc., updated every ~1 minute.

Log.out - a running log from STAR, with information about the run.

Aligned.sortedB圜 - the aligned reads, sorted by coordinate, in BAM format.

- a summary of mapping statistics for the sample.

Briefly, these files are described below: What you should see, is that for each FASTQ file you have 5 output files and a single tmp directory.

Remote utilities viewer screen not aligning