Daniel:Notebook/GenomeMiner/2013-9-17: Difference between revisions
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>Djacobse (Created page with "=Mock HL155 (Started 9/9/2013)= Back to Calendar ==High Deletion Rate Test== Checking the results f...") |
>Djacobse |
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3. hl155bash.sh | 3. hl155bash.sh | ||
4. perl imp_count_mismatch.plx (Matt's error counting script) | 4. perl imp_count_mismatch.plx (Matt's error counting script) | ||
===Alignment Results=== | |||
2959000 reads; of these: | |||
2959000 (100.00%) were unpaired; of these: | |||
523061 (17.68%) aligned 0 times | |||
2431720 (82.18%) aligned exactly 1 time | |||
4219 (0.14%) aligned >1 times | |||
82.32% overall alignment rate | |||
So much poorer alignment than high substitutions, but still overall a high rate. |
Revision as of 20:28, 17 September 2013
Mock HL155 (Started 9/9/2013)
High Deletion Rate Test
Checking the results from the previous run by redoing the data, this time using a lower substitution rate and a higher deletion rate. Substitutions: 0.05%, Insertions: 0.26%, Deletions, 1.01%.
Workflow
1. MockHL155_Master.m, Switch 2 2. scp v4s1_mockseq_1s.fq djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/mockseq/error1s/ 3. hl155bash.sh 4. perl imp_count_mismatch.plx (Matt's error counting script)
Alignment Results
2959000 reads; of these: 2959000 (100.00%) were unpaired; of these: 523061 (17.68%) aligned 0 times 2431720 (82.18%) aligned exactly 1 time 4219 (0.14%) aligned >1 times 82.32% overall alignment rate
So much poorer alignment than high substitutions, but still overall a high rate.