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# SamSifter Help

## Manual

- SamSifter Manual
  - Detailed Installation Instructions
    - Installing `Python3` and `PyQt4`
      - Debian 8 (jessie) and newer or Ubuntu 14.04 and newer
      - Older Debian or Ubuntu systems
      - Mac OS X using Homebrew
      - Windows (32 bit)
    - Installing SamSifter
    - Uninstalling SamSifter
  - Creating and Editing Workflows
    - Selecting an Input File
    - Adding and Removing a Tool or Filter
    - Rearranging Tools and Filters
    - Displaying and Editing Filter Settings
    - Selecting an Output File
      - Optional: Creating an RMA file for MEGAN
  - Executing Workflows
    - Running a Workflow
    - Log Messages
    - Stopping a Workflow
  - Loading and Saving Workflows
  - Export to Bash scripts
  - Manuals for Filters and Tools
    - Common Options
    - Count reads per taxon
    - Filter reads by conservation
    - Filter reads by list of QNAMES
    - Filter references by evenness of coverage
      - What is the Gini coefficient?
      - Experimental options
    - Filter references by % identity
    - Filter references by list of accessions
    - Filter references by PMD score
    - Filter taxa by list of taxon IDs
    - Filter taxa by PMD score
    - [GNU gzip] Compress file
    - [GNU gzip] Decompress file
    - [PMDtools] Calculate PMDS
    - [PMDtools] Filter reads by % identity
    - [PMDtools] Filter reads by PMDS
    - [SAMtools] Convert BAM to SAM
    - [SAMtools] Convert SAM to BAM
    - [SAMtools] Remove duplicates
    - [SAMtools] Sort by coordinates
    - [SAMtools] Sort by query names
    - [BetterRMDup] Remove duplicates
  - Statistical Summaries
    - Compiling Results Per Analysed File
    - Comparison of Multiple Files
    - Enriching Summaries with External Databases

## Frequently Asked Questions

None so far...

## Known Bugs

Please report new bugs to f.aldehoff@student.uni-tuebingen.de.

### Bugs in SamSifter

- The ‘Export to Bash’ dialog fails to save the file when SamSifter has been started from the GNOME/KDE/Unity menu. Saving SSX files works fine, however. Workaround: Save Workflow to SSX, close SamSifter, open SamSifter from Shell and retry exporting the Bash script.

### Bugs in Tools used by SamSifter

- BetterRMDup fails when processing MALT’ed files. This is actually a bug of the SAM parsing library used in BetterRMDup that does not handle the custom MALT `@mm` record properly. The bug has been reported and will be fixed in a future version.
- SAMtools `view` reports a possibly truncated file and complains about a missing EOF marker. This is likely a bug in either MALT and/or SAMtools `view` which can be safely ignored. See http://sourceforge.net/p/samtools/mailman/samtools-help/thread/4EC52844.3090808@broadinstitute.org/ for details. It is caused by a missing compression flag when processing uncompressed files.
- SAMtools `view` complains about inconsistency of the sequence length when compared to the CIGAR string. This is a bug in MALT 0.0.12 that has been reported. Please re-MALT your files with a newer version or remove the affected reads manually.

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