lecture_notes:04-30-2010
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lecture_notes:04-30-2010 [2010/05/05 20:53] jmagasin |
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| From Jonathan Magasin. | From Jonathan Magasin. | ||
| - | Today's lecture covered files generated by Kevin's map-colorspace5 | + | Today's lecture covered files generated by Kevin's map-colorspace5\\ |
| - | script which will be necessary for the homework assignment: ordering | + | script which will be necessary for the homework assignment: ordering\\ |
| - | the POG contigs. Also covered: How to roughly estimate banana slug | + | the Pog contigs. Also covered: How to roughly estimate banana slug\\ |
| genome size. | genome size. | ||
| - | ==== Homework assignment: assemble POG ==== | + | ==== Homework assignment: assemble Pog ==== |
| - | From the newer newbler we have a different set of contigs, thirty-one | + | From the newer newbler we have a different set of contigs, thirty-one\\ |
| - | of them. We also have mate pairs from SOLiD mapped to newbler | + | of them. We also have mate pairs from SOLiD mapped to newbler\\ |
| - | assembly 5. The assignment is to order and orient them the contigs. | + | assembly 5. The assignment is to order and orient them the contigs.\\ |
| - | Kevin has posted his solution in the assembly directory | + | Kevin has posted his solution in the assembly directory\\ |
| (assemblies/Pog/map-colorspace5). | (assemblies/Pog/map-colorspace5). | ||
| === 'delete' and 'invert' files === | === 'delete' and 'invert' files === | ||
| - | The trim9 files are output from Kevin's map-colorspace5 script. Most | + | The trim9 files are output from Kevin's map-colorspace5 script. Most\\ |
| - | of them are not for us. The 'delete' files are for mate pairs where | + | of them are not for us. The 'delete' files are for mate pairs where\\ |
| - | both mapped but not at the appropriate distance: closer than 350 | + | both mapped but not at the appropriate distance: closer than 350\\ |
| - | bases, or more than 5000 bases apart. These files can be studied to | + | bases, or more than 5000 bases apart. These files can be studied to\\ |
| find massive deletions. | find massive deletions. | ||
| - | 'invert' files are for mate pairs that were on opposite strands (at | + | 'invert' files are for mate pairs that were on opposite strands (at\\ |
| - | any distance) and are useful for studying inversions. However | + | any distance) and are useful for studying inversions. However\\ |
| - | inversions are not so useful because they will not be within a single | + | inversions are not so useful because they will not be within a single\\ |
| contig. | contig. | ||
| - | The 'between contigs' files are for when the reads mapped to different | + | The 'between contigs' files are for when the reads mapped to different\\ |
| - | contigs. Only cases with unique mappings are in these files. fixme: | + | contigs. Only cases with unique mappings are in these files. fixme:\\ |
| What file(s) is this? | What file(s) is this? | ||
| === trim9.out === | === trim9.out === | ||
| - | The trim9.out file is a summary of what happened during mapping. | + | The trim9.out file is a summary of what happened during mapping.\\ |
| - | Kmers are colorspace kmers. These kmers are the lengths after | + | Kmers are colorspace kmers. These kmers are the lengths after\\ |
| - | trimming off nine. 'uniquly mapped' means one for the R3 and one for | + | trimming off nine. 'uniquly mapped' means one for the R3 and one for\\ |
| - | the F3. Note that some of the summary stats are bugs (the 'wrong | + | the F3. Note that some of the summary stats are bugs (the 'wrong\\ |
| - | range' line) that have since been fixed. [Kevin reran the script of | + | range' line) that have since been fixed. [Kevin reran the script of\\ |
| Friday.] | Friday.] | ||
| Compared to earlier mapping, Kevin has increased the agressiveness. | Compared to earlier mapping, Kevin has increased the agressiveness. | ||
| - | The deletions ('wrong range' line) appear to be from reads taken from | + | The deletions ('wrong range' line) appear to be from reads taken from\\ |
| clones with multiple adapters. | clones with multiple adapters. | ||
| - | Strand biases (algorithmic) were checked for in the forward and | + | Strand biases (algorithmic) were checked for in the forward and\\ |
| backward counts of mapped reads. | backward counts of mapped reads. | ||
| - | Tonight Kevin [reran] the mapping script. The new output will | + | Tonight Kevin [reran] the mapping script. The new output will\\ |
| - | include error rates by position. Sol requested these be called | + | include error rates by position. Sol requested these be called\\ |
| - | mismatches rather than errors. Kevin said they are estimates of | + | mismatches rather than errors. Kevin said they are estimates of\\ |
| - | sequencing error. They are in colorspace, and exclude indels. In | + | sequencing error. They are in colorspace, and exclude indels. In\\ |
| - | reality they are differences between the reads and assemblies, not | + | reality they are differences between the reads and assemblies, not\\ |
| - | errors. But for all practical purposes when there is a mismatch | + | errors. But for all practical purposes when there is a mismatch\\ |
| between a read and the assembly the error is in the read.) | between a read and the assembly the error is in the read.) | ||
| === trim9.joins === | === trim9.joins === | ||
| - | The data we'll use is not in trim9.out, rather it is in trim9.joins. | + | The data we'll use is not in trim9.out, rather it is in trim9.joins.\\ |
| - | trim9.joins is computed from trim9-cross.rdb (which has reads that | + | trim9.joins is computed from trim9-cross.rdb (which has reads that\\ |
| crossed a contig boundary). | crossed a contig boundary). | ||
| - | Looking at the first line: How many reads support contig 22 following | + | Looking at the first line: How many reads support contig 22 following\\ |
| - | contig 3? 34K. The contigs lengths are there to see if a contig is | + | contig 3? 34K. The contigs lengths are there to see if a contig is\\ |
| - | short enough that mate pairs might span them. E.g. what orderings are | + | short enough that mate pairs might span them. E.g. what orderings are\\ |
| - | consistent with the listed contig orders: 2->3->4, or maybe 3 is very | + | consistent with the listed contig orders: 2->3->4, or maybe 3 is very\\ |
| short so we have a mate pair that jumps over 3. | short so we have a mate pair that jumps over 3. | ||
| - | A minus sign appearing before a contig name means to take the | + | A minus sign appearing before a contig name means to take the\\ |
| - | reverse-complement of that contig. (And contig3 followed by contig22 | + | reverse-complement of that contig. (And contig3 followed by contig22\\ |
| is the same as -contig22 followed by -contig3.) | is the same as -contig22 followed by -contig3.) | ||
| - | The last number on each line indicates if the mate pair were the | + | The last number on each line indicates if the mate pair were the\\ |
| - | optimal length (optimal is the peak of length distribution). That | + | optimal length (optimal is the peak of length distribution). That\\ |
| - | number is the expected length of the gap between the contigs. It is | + | number is the expected length of the gap between the contigs. It is\\ |
| very rough. | very rough. | ||
| - | The file is sorted most-counts to fewest. The stuff at bottom of the | + | The file is sorted most-counts to fewest. The stuff at bottom of the\\ |
| file is noise. Only about first fifty lines are helpful. | file is noise. Only about first fifty lines are helpful. | ||
| - | Long mate pairs are very helpful for disambiguating, and wish we had | + | Long mate pairs are very helpful for disambiguating, and wish we had\\ |
| - | them for H.pylori. | + | them for //H.pylori//. |
| === Your task === | === Your task === | ||
| - | Take the trim9.joins file and try to order and orient the contigs, | + | Take the trim9.joins file and try to order and orient the contigs,\\ |
| - | knowing that some of them are duplicated, and that there is a virus in | + | knowing that some of them are duplicated, and that there is a virus in\\ |
| the mix and there should be one large chromosome. | the mix and there should be one large chromosome. | ||
lecture_notes/04-30-2010.1273092831.txt.gz · Last modified: 2010/05/05 20:53 by jmagasin
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