Mercurial > repos > mvdbeek > mismatch_frequencies
changeset 18:e3d950e52e38
Uploaded
| author | mvdbeek |
|---|---|
| date | Mon, 11 May 2015 07:45:10 -0400 |
| parents | deac50041967 |
| children | f7da7f3e2c98 |
| files | mismatch_frequencies.xml test-data/mismatch.pdf test-data/mismatch.tab |
| diffstat | 3 files changed, 37 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/mismatch_frequencies.xml Wed Apr 01 08:35:11 2015 -0400 +++ b/mismatch_frequencies.xml Mon May 11 07:45:10 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.6" hidden="false" > +<tool id="mismatch_frequencies" name="Mismatch Frequencies" version="0.0.7" hidden="false" > <description>Analyze mismatch frequencies in BAM/SAM alignments</description> <requirements> <requirement type="package" version="0.7.7">pysam</requirement> @@ -35,8 +35,41 @@ <tests> <test> <param name="rep_0|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" /> - <param name="rep_1|input_file" value="3mismatches_ago2ip_s2.bam" ftype="bam" /> + <param name="rep_1|input_file" value="3mismatches_ago2ip_ovary.bam" ftype="bam" /> <param name="number_of_mismatches" value="1" /> <param name="min_length" value="21" /> <param name="max_length" value="21" /> + <param name="three_p" value="0" /> + <param name="five_p" value="0" /> + <output name="tabular" file="mismatch.tab" ftype="tabular"/> + <!-- + <output name="pdf" file="mismatch.pdf" ftype="pdf"/> + --> + </test> + </tests> + <help> + +.. class:: infomark + + +***What it does*** + +This tool reconstitues for each aligned read of an alignment file in SAM/BAM format whether +a mismatch is annotated in the MD tag, and if that is the case counts the identity of the +mismatch relative to the reference sequence. The output is a PDF document with the calculated +frequency for each mismatch that occured relative to the total number of valid reads and a table +with the corresponding values. Read length can be limited to a specific read length, and 5 prime and +3 prime-most nucleotides of a read can be ignored. + +---- + +.. class:: warningmark + +***Warning*** + +This tool skips all read that have insertions and has been tested only with bowtie and bowtie2 +generated alignment files. + +Written by Marius van den Beek, m.vandenbeek at gmail . com + </help> </tool>
--- a/test-data/mismatch.tab Wed Apr 01 08:35:11 2015 -0400 +++ b/test-data/mismatch.tab Mon May 11 07:45:10 2015 -0400 @@ -1,3 +1,3 @@ library readsize A to C A to G A to T C to A C to G C to T G to A G to C G to T T to A T to C T to G total valid reads -3mismatches_ago2ip_s2.bam 21 31 5484 69 25 40 137 156 109 188 51 196 29 43881 -3mismatches_ago2ip_ovary.bam 21 293 879 411 452 231 872 845 191 473 384 818 324 138649 +3mismatches_ago2ip_s2.bam 21 48 6503 106 68 46 173 222 144 220 90 232 40 43881 +3mismatches_ago2ip_ovary.bam 21 380 1214 524 581 278 1127 1032 239 595 483 973 394 138649