archive:bioinformatic_tools:bwa
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archive:bioinformatic_tools:bwa [2011/05/13 03:01] svohr created |
archive:bioinformatic_tools:bwa [2011/05/13 06:06] karplus Questions about discrepancy on insert length |
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| Their are two options for the algorithm. The default option, ''is'', is relatively fast and works on genomes smaller than 2GB. The other algorithm, ''bwtsw'', is slower and less accurate but works on longer reads and works with larger databases. | Their are two options for the algorithm. The default option, ''is'', is relatively fast and works on genomes smaller than 2GB. The other algorithm, ''bwtsw'', is slower and less accurate but works on longer reads and works with larger databases. | ||
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| Next, the reads are aligned to the reference using the ''aln'' command. | Next, the reads are aligned to the reference using the ''aln'' command. | ||
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| bwa sampe database.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln.sam | bwa sampe database.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln.sam | ||
| </code> | </code> | ||
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| + | ====== Determining Paired-End Insert Size ====== | ||
| + | BWA was used to estimate the distribution of insert sizes in the Illumina runs for banana slug. The 454 reads were used as the reference and the Illumina reads were mapped onto them. The distribution of the insert lengths can be inferred from the pairs that map onto the same 454 read. This is possible because our insert sizes are smaller than the size of the 454 reads. | ||
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| + | Here is the frequencies of each inferred insert length from the SAM file from the paired end alignments for Illumina run 2. The mean inferred insert size for the barcode 7 reads is 258 bases and 138 bases for the barcode 8 reads. Note that this differs considerably from the estimates of 411 bp for barcode 7 and 372bp for barcode 8 from the [[computer_resources:data|computer_resources:data]] page, which was based on bioanalyzer results for the DNA library. What is the discrepancy? Is it different definitions of the length (including neither, one, or both reads in the length)? Why does the barcode 8 graph cut off so abruptly? (overlapping reads?) If the "inferred insert length" here is between the reads, then we need to add 200 for the read lengths to get the full DNA length, giving 458 and 338, which are fairly close to numbers reported by the bioanalyzer, but that would not explain the cutoff at 100. If the inferred insert length here is the difference in the start positions in the same strand of the two reads, we would have to add 100 for the read length, getting 354 and 238, which seem a bit low. | ||
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| + | So what exactly is the "inferred insert length" being plotted here? FIXME | ||
| + | {{:bioinformatic_tools:run2_insert_size_histogram.png|}} | ||
archive/bioinformatic_tools/bwa.txt · Last modified: 2015/09/04 09:06 by 68.180.228.52
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