comparison PEsortedSAM2readprofile.xml @ 5:b27006b0a953

update to latest version

4:ecfc9041bcc5

<tool id="PEsortedSAM2readprofile" name="Combine mapped flaked bases" version="1.0.0">
  <description> from SAM file sorted by readname  </description>
  <command interpreter="python2.7">PEsortedSAM2readprofile.py  $flankedbasesSAM $twobitref $maxTRlength $maxoriginalreadlength $output </command>

  <inputs>
    <param name="flankedbasesSAM" type="data" format="sam" label="Select sorted SAM file (by readname) of flaked bases" />
    <param name="twobitref" type="data" label="Select twobit file reference genome" />

.. class:: infomark

**What it does**

- This tool will take SAM file sorted by read name, remove unpaired reads, report microsatellites sequences in the reference genome that correspond to the space between paired end reads. Coordinate of start and stop for left and right flanking regions of microsatellites and microsatellite itself as inferred from paired end reads will also be reported.
- These microsatellites in reference can be used to filter out reads that do not contain microsatellites that concur with microsatellites in reference where the reads mapped to.

**Citation**

When you use this tool, please cite **Arkarachai Fungtammasan and Guruprasad Ananda (2014).**
 
**Input**

- Sorted SAM files by read name

**Output**

The output will combined two lines of input which are paired. The output format is as follow.

- Column 1 = read name
- Column 2 = chromosome 
- Column 3 = left flanking region start
- Column 4 = left flanking region stop
- Column 5 = microsatellite start
- Column 6 = microsatellite stop
- Column 7 = right flanking region start
- Column 8 = right flanking region stop
- Column 9 = microsatellite length in reference
- Column 10= microsatellite sequence in reference



</help>
</tool>

5:b27006b0a953

<tool id="PEsortedSAM2readprofile" name="Combine mapped faux paired-end reads" version="1.0.0">
  <description> and get the reference STR allele from the reference genome  </description>
  <command interpreter="python2.7">PEsortedSAM2readprofile.py  $flankedbasesSAM $twobitref $maxTRlength $maxoriginalreadlength $output </command>

  <inputs>
    <param name="flankedbasesSAM" type="data" format="sam" label="Select sorted SAM file (by readname) of flaked bases" />
    <param name="twobitref" type="data" label="Select twobit file reference genome" />

.. class:: infomark

**What it does**

- This tool will take SAM file (sorted by read name), remove unpaired reads, and combine paired faux read-pairs into a single row. It also reports Short Tandem Repeats (STRs) sequences in the reference genome that correspond to the space between the faux paired end reads and the coordinate of start and stop for left and right flanking regions of STRs.

**Citation**

When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
 
**Input**

- Sorted SAM files by read name. 

**Output**

The output will combine the two faux paired-end read lines of input ito the following single line format:

- Column 1 = read name
- Column 2 = chromosome 
- Column 3 = left flanking region start
- Column 4 = left flanking region stop
- Column 5 = STR start
- Column 6 = STR stop
- Column 7 = right flanking region start
- Column 8 = right flanking region stop
- Column 9 = STR length in reference
- Column 10= STR sequence in reference



</help>
</tool>