Workflow Wednesdays – Part 3. Read preprocessing – Trimming

07/08/2013

With “short” reads getting longer and longer, read trimming seems to be more and more useful. In my experience, long reads tend to have a significant quality drop at the read end, regardless of sequencing platform, so it makes sense to trim these low quality parts off.

Workflow Wednesdays – Part 3. Read preprocessing – Filtering

31/07/2013

After last weeks post about randomly subsampling fastq files, let’s take a look at a different method for making read files smaller.

Workflow Wednesdays – Part 3. Read preprocessing – Adaptor trimming

17/07/2013

After a few weeks long sidetrack about reference sequence manipulation, let’s get back to our reads. If you’ve read my post about read quality control results, you might remember, that I found some untrimmed adaptors on the 454 reads (SRR797242.fastq). In this post, I’ll show you a few ways...

Workflow Wednesdays – Part 3. Read preprocessing – Read quality control 2. – QC results

26/06/2013

Text output Both FastQC and PRINSEQ can generate some basic statistics for each fastq file. For FASTQC these are the following: “Total Sequences” (i.e. the number of reads), “Filtered Sequences”, “Sequence Length” (read length range) and “%GC” (average GC-content). Additionally, tables for “Overrepresented sequences” and “Kmer content” are generated....

Workflow Wednesdays – Part 3. Read preprocessing – Read quality control 1. – Running QC tools

19/06/2013

Read quality control tools can provide very useful information about the the success of your sequencing experiment, without the need to run time consuming alignments and variant calls. Based on read length, per base quality, base content and other basic statistics you can find out a lot about your...