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BulkSeq Studio 0.14.0

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@tunabirgun tunabirgun released this 26 Jun 19:13
v0.14.0
3d1a78a

BulkSeq Studio 0.14.0

A full audit of the GUI controls and analysis scripts (multi-agent, adversarially verified) found no scientific-validity issues — the DESeq2 baseline reproduces exactly — and turned up two GUI controls that looked active but did nothing. Both now work.

Added

  • Skip-trimming toggle. The "fastp trimming" checkbox is now honored: unchecking it skips fastp entirely and sends the raw reads straight to the aligner (and to rRNA filtering, if that is on). Previously the box only changed the runtime estimate while fastp always ran. FastQC-before/after and the MultiQC inputs follow the same gating. Leave it on unless your reads are already trimmed.
  • GFF3 annotation support. The annotation Format selector (gtf / gff3) is now honored: a GFF3 annotation is converted to GTF with gffread before indexing and counting, so STAR/HISAT2/Salmon and featureCounts get the GTF they expect. Previously selecting gff3 did nothing and a real GFF3 file was silently parsed as GTF (wrong or empty counts). The GTF path is unchanged.

Validation

The default (trimming-on, GTF) path is byte-identical: the F. graminearum DESeq2 baseline still reproduces 2723 up / 2478 down. Trimming-off was run end to end (raw reads → aligner → counts), the trimming-off + rRNA-on combination routes raw reads into SortMeRNA, and a GFF3→GTF round trip is count-identical to the original GTF (featureCounts assigns the same reads to the same genes).

Downloads

Windows:

  • BulkSeqStudio-Setup-0.14.0.exe — installer
  • BulkSeqStudio-Portable-0.14.0.zip — unzip and run BulkSeqStudio.exe, no install

Linux (x86-64, glibc 2.39+):

  • BulkSeqStudio-0.14.0-x86_64.AppImage — mark executable and run
  • BulkSeqStudio-linux-0.14.0.tar.gz — extract and run BulkSeqStudio
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