v2.6.4

Minor update, mostly associated with speed boosts. A small tweak to samtools should actually be realized in a large speed increase, particularly for big genomes.

Bug fixes and better output organization

• Several bugs were fixed
• Output folders were created for better organization
• Fixed fastqc_out redirect error

Support for Transcriptome assembly

The major changes in this version are:

• Support for transcriptome assembly (Salmon)
• Gff is optional

Minor improvements

Minor improvements are made to this version

Small bug fixes

Fixed typos, moved files and removed unnecessary files that are not needed for the tool

Feature counts options added

Updated RMTA major release version (v2.5) with few minor changes which includes options for features such as feature type, gene attribute, and strandedness.
Fixed typos and removed unnecessary files.

Major RMTA version release

This is a major release of RMTA with several features added and removed some features because they are either too old or no longer is not needed.

Major changes (Additions):

• Bowtie2 v2.3.5 has been added. This version has the support of SRA and so can be used to map the reads on the fly without downloading them.
• Added Fastqc support. With this, now you can check to see the quality of the reads before and after trimming the reads using the options provided with Hisat2 and Bowtie2.
• Modified Dockerfile and replaced the software binaries with conda package installations.
• Added support for removing duplicate reads using Picard MarkDuplicates option.
• RMTA 2.5 now requires that you specify the type of reads (SE and PE).
• RNA strandedness option has now the default "unstranded" option.
• Replaced Sorghum test data with Arabidopsis test data.
• The default option to generate read counts using featurecounts.

Major changes (Removals):

• Removed Cufflinks and the only transcript assembler is now StringTie.

Updated RMTA release with minor bug fixes

Some minor bugs have been found and have been fixed in this version

Updated RMTA release

RMTA has been updated significantly by updating the version of the tools such as

• Sambamaba
• Samtools
• Hisat2

In addition, we have included an additional option to filter the transcripts based on FPKM (in addition to coverage cut-off), captured the metrics and mapping results in a file and finally print messages for the step that are running.

Minor bug fix to v1.6

Merge pull request #1 from Evolinc/andrew-d-l-nelson-patch-1

Update Hisat2-Cuffcompare-Cuffmerge.sh