archive:bioinformatic_tools:bwa
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archive:bioinformatic_tools:bwa [2015/08/03 01:18] 66.249.79.241 ↷ Links adapted because of a move operation |
archive:bioinformatic_tools:bwa [2015/09/04 09:06] (current) 68.180.228.52 ↷ Links adapted because of a move operation |
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| 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. | 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. | ||
| - | 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? The difference is that the Bioanalyzer results include the adapters, not just the DNA that is sequenced, so the difference is actually fairly small. | + | 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 [[archive:computer_resources:data|computer_resources:data]] page, which was based on bioanalyzer results for the DNA library. What is the discrepancy? The difference is that the Bioanalyzer results include the adapters, not just the DNA that is sequenced, so the difference is actually fairly small. |
| Why does the barcode 8 graph cut off so abruptly? (overlapping reads?) | Why does the barcode 8 graph cut off so abruptly? (overlapping reads?) | ||
archive/bioinformatic_tools/bwa.1438564735.txt.gz · Last modified: 2015/08/03 01:18 by 66.249.79.241
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