Supplementary Materials

These are supplementary files for the PiGx paper. All reports were generated with PiGx 0.0.3 as installed with GNU Guix at version v0.14.0-7054-g5149aeb7e (git commit 5149aeb7e62cf62398b55be38469cd28c25d8d7d).

We provide a generated Docker image on Dockerhub. The tag bimsbbioinfo/pigx:publication corresponds to the image at the above Guix version, which was used for the publication.

We also provide a SquashFS file system image, which can be used with systems like Singularity.

The SquashFS image was created with this command:

guix pack pigx            \
          -f squashfs     \
          -S /bin=bin     \
          -S /lib=lib     \
          -S /share=share \
          glibc-utf8-locales tzdata coreutils bash

This command was used for generating the Docker image:

guix pack pigx            \
          -f docker       \
          -C none         \
          -S /bin=bin     \
          -S /lib=lib     \
          -S /share=share \
          glibc-utf8-locales tzdata coreutils bash

PiGx scRNA-seq

The HTML report output of the scRNA-seq pipeline from the analysis of the single cell sequencing dataset from (Hu et al. 2017) can be accessed here.

An archive containing a sample sheet, settings file, and instructions on how to reproduce the report can be downloaded here.

PiGx ChIP-seq

The HTML report output of the ChIP-seq pipeline from the analysis of the ChIP-seq datasets from Hon. et al can be accessed here.

An archive containing a sample sheet, settings file, and instructions on how to reproduce the report can be downloaded here.

PiGx RNA-seq

Below are links for the HTML reports for each differential expression analysis performed using STAR-based gene counts for the use-case RNA-seq datasets:

• tet2_diff_day3

• tet2_diff_day6

• tet2_vs_WT_day0

• tet2_vs_WT_day3

• tet2_vs_WT_day6

• WT_diff_day3

• WT_diff_day6

An archive containing a sample sheet, settings file, and instructions on how to reproduce the report can be downloaded here.

PiGx BS-seq

The supplementary results for the BS-seq pipeline from the analysis of the RNA-seq datasets from Hon. et al consist of three reports in HTML format; We have highlighted the most important figures from the study.

Each HTML document represents a stand-alone summary of some the key findings for the given sample, along with a description of the key operations carried out by the pipeline.

• Tet2 deletion (biological replicate 1) report

• Wild-type (biological replicate 1) report

• Differential methylation, biological replicate 1, (tet2-/-) - WT

An archive containing a sample sheet, settings file, and instructions on how to reproduce the report can be downloaded here.

About PiGx

PiGx is free software under the GNU General Public License (version 3 or, at your option, any later version). You can get the complete source code here. Your contributions are welcome!

Consider subscribing here to infrequent announcements regarding PiGx, such as release announcements.