Wed Apr 8
Forward reads sw019_s1_l001_r1_001.fastq_fastqc_report.pdf
Reverse reads sw019_s1_l001_r2_001.fastq_fastqc_report.pdf
Fastqc detected two issues with the reads: a) the per base sequence quality of reads decreases at the end of reads, and b) there are several over-represented k-mers in the data (possibly adaptor sequences).
Fri Apr 10
Chris Eisenhart - Looking at the Preqc results, I do not see the banana slug data in the first three slides. The banana slug is indicated to be blue by the index, but I do not see it on these graphs. Could this due to a hard coded X and Y ranges that do not include the banana slug data?
The preqc output is slightly strange, likely because of the low coverage. Preqc estimated a genome size of ~1600 Mbp.
Fri Apr 17
These data with the adapters removed are located at
The fastq to bam conversion was performed using the picard toolset. Specifically the fastqToSam.jar file was used to prepare the bam files.
This section contains various notes I've made when doing a second pass in analyzing the presence of potential adapter sequences in the raw .fastq datasets.
For forward (R1) strands:
For reverse (R2) strands:
The data files were trimmed using SeqPrep, both with and without merging. The output for the run without merging is in /campusdata/BME235/Spring2015Data/adapter_trimming/SeqPrep and the output for the run with merging is in /campusdata/BME235/Spring2015Data/merging/SeqPrep. The trimmed R1 and R2 files for the run with merging are smaller than those from the non-merging run, but the difference is much smaller than with SW018_1 and the merged file is much larger.
The adapters used for both runs were AGATCGGAAGAGCACACGTCTGAACTCCAG (-A option) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAG (-B option).
All SW019 data sets that had been adapter trimmed using Seqprep were merged with Fastuniq to remove duplicates and then error corrected using Musket