lecture_notes:04-28-2010
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lecture_notes:04-28-2010 [2010/05/02 05:01] galt |
lecture_notes:04-28-2010 [2010/05/02 05:34] galt |
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| + | John St. John's lecture on EULER-SR and Celera; Michael Cusack's lecture on MIRA | ||
| + | |||
| === Misc Notes: === | === Misc Notes: === | ||
| Line 12: | Line 14: | ||
| - | Kevin | + | Kevin mapped newbler to join the contigs |
| - | I mapped newbler to join the contigs | + | |
| found a bug in the python script to map the solid reads. | found a bug in the python script to map the solid reads. | ||
| Detected because there were no joining reads | Detected because there were no joining reads | ||
| Line 33: | Line 34: | ||
| that can use long reads and mate-pairs. | that can use long reads and mate-pairs. | ||
| - | ran well first time (it ran, at least) \\ | + | **euler-sr-assembly1/**\\ |
| - | have to run it where you installed it \\ | + | Ran on 454 data with the Sanger data concatenated into one file. |
| - | no makefiles \\ | + | |
| - | result: \\ | + | Have to set up env vars.\\ |
| + | No make install options.\\ | ||
| + | Things are mixed up.\\ | ||
| + | You have to run it where you installed it \\ | ||
| + | ${EUSRC}\\ | ||
| + | |||
| + | It ran well the first time (it ran, at least) \\ | ||
| + | |||
| + | ${EUSRC}/assembly/Assemble.pl pogreads.fasta 25\\ | ||
| + | |||
| + | **Result**: \\ | ||
| ~2k contigs which create a 2x long genome… suspicious \\ | ~2k contigs which create a 2x long genome… suspicious \\ | ||
| are contigs overlapping? \\ | are contigs overlapping? \\ | ||
| //find out:// \\ | //find out:// \\ | ||
| - | check blat_strict_match (blat alignment to reference genome) \\ | + | check contig-blat_strict_match (blat alignment to reference genome) \\ |
| look for "Q name" (contigs) which match to the same "T start" positions on the reference genome \\ | look for "Q name" (contigs) which match to the same "T start" positions on the reference genome \\ | ||
| //answer://yes, appear to overlap a lot – double coverage because they totally overlap | //answer://yes, appear to overlap a lot – double coverage because they totally overlap | ||
| + | |||
| + | There is one 91k contig.\\ | ||
| Things to try to improve the run: \\ | Things to try to improve the run: \\ | ||
| - | - longer k-mers \\ | + | - longer k-mers, increasing to 31 should be easy \\ |
| - increase frequency threshold (help make up for read errors, maybe?) \\ | - increase frequency threshold (help make up for read errors, maybe?) \\ | ||
| + | - throw out the tiny contigs, reduce your cutoff. | ||
| + | |||
| + | Does have an option to do some simple quality filtering on the reads\\ | ||
| + | if quality data such as fastq is used?\\ | ||
| + | -minmult look at how many things map to this area,\\ | ||
| + | if less than this many things, throw it out.\\ | ||
| + | |||
| + | Error-correct reads, construct repeat graph,\\ | ||
| + | simplifiy repeat graph with mate-reads\\ | ||
| + | Error correction by threading.\\ | ||
| + | Tries to make minimal corrections to beginnings of reads,\\ | ||
| + | uses those to make the kmers. Later threads the full readlength through. | ||
| "Error Correction via threading" \\ | "Error Correction via threading" \\ | ||
| Line 55: | Line 79: | ||
| - perhaps this is where it went wrong? \\ | - perhaps this is where it went wrong? \\ | ||
| + | Mate reads.\\ | ||
| + | Multiple paths of similar length are hard to disambiguate.\\ | ||
| + | You can use multiple matepairs and bootstrap analysis.\\ | ||
| + | Use the paths with the highest probability.\\ | ||
| + | |||
| + | Pog repeats aside:\\ | ||
| + | There are several large homologous regions on opposite strands\\ | ||
| + | in Pog data that are kinds of repeats. \\ | ||
| + | They are at both ends of the area that inverts.\\ | ||
| + | Inversion happens by homologous matching, then swapping by two strands.\\ | ||
| + | Like a sloppy integrase. | ||
| + | |||
| + | |||
| + | **Solid data.**\\ | ||
| + | Used the regular base-space data in colorspace_input.fa (not double-encoded).\\ | ||
| Tried to run on just the SOLiD data… started on Sunday, but still running (Wed) \\ | Tried to run on just the SOLiD data… started on Sunday, but still running (Wed) \\ | ||
| Line 60: | Line 99: | ||
| === Celera Assember: === | === Celera Assember: === | ||
| - | needs qual info (need this from Sanger reads, too) \\ | + | **Result**: \\ |
| - | ... so can't run unless you have the .qual files | + | Celera on Pog 454 got 2.4M genome. 386 contigs. Max size 34k.\\ |
| + | Needs quality information also, even for the Sanger reads \\ | ||
| + | So can't run unless you have the .qual files | ||
| + | |||
| + | Script for converting Illumina (Solexa) reads into their format but not released yet.\\ | ||
| + | Their next release is supposedly soon (May 1st). | ||
| + | |||
| + | They have settings for sungrid running, but it did not work,\\ | ||
| + | so he turned it off. | ||
| - | seemed to have a script to convert Illumina -> their format… but not released yet | + | How noisy is the solid data? (Kevin)\\ |
| + | On the stuff that maps completely, about 1.5% err rate.\\ | ||
| + | The ones that didn't map cleanly had error-rate 2.5%.\\ | ||
| + | Error rate goes up at the end.\\ | ||
| + | Had some fluidics reads problems at some base positions. | ||
| - | result: \\ | + | Took about 50 minutes for all.\\ |
| - | with 454 data alone: 386 contigs \\ | + | For comparison, Newbler took 18 minutes and about 40 contigs. |
| - | (newbler: ~40 contigs) \\ | + | |
| - | took about 50min | + | Just qsub them with no arguments, and it runs everything.\\ |
| - | === Mira === | + | === MIRA === |
| - | needs datafile named pog_in.[format].fa \\ | + | Needs datafile named pog_in.[format].fa \\ |
| sff_extract script to create .qual files | sff_extract script to create .qual files | ||
lecture_notes/04-28-2010.txt · Last modified: 2010/05/02 16:22 by karplus
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