Anton Kulaga antonkulaga
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| java -jar ./trimmomatic-0.33.jar SE -threads 2 -phred33 /home/antonkulaga/data/raw/flies/fastq/3_TTAGGC_L003_R1_001.fastq /home/antonkulaga/data/raw/flies/cleanup/3_trm.fastq ILLUMINACLIP:/opt/trimmomatic/adapters/TruSeq2-SE.fa:2:30:10 SLIDINGWINDOW:4:25 |
antonkulaga
/ gist:d0c76a2cd6e6de55b9af
Last active
August 29, 2015 14:18
transcriptome assembly with Scythe-Sickle-Hisat-Stringtie-Ballgrown
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| ###IMPROVING FASTQ (note: apply the same to all your fastq files) ### | |
| #deleting illumina adapters by https://github.com/vsbuffalo/scythe | |
| ./sickle se -f /home/uploader/flies/assembly4/3_cleaned.fastq -t sanger /home/uploader/flies/assembly4/3.fastq | |
| #triming fastq by https://github.com/najoshi/sickle | |
| sickle se -f /home/uploader/flies/assembly4/3_cleaned.fastq -t sanger -o /home/uploader/flies/assembly4/3.fastq -q 25 | |
| ### Hisat http://ccb.jhu.edu/software/hisat/manual.shtml ### |
antonkulaga
/ gist:fdbd6a1ef43a0f188c55
Last active
August 29, 2015 14:18
transcriptome assembly with Scythe-Sickle-Bowtie-Tophat-Stringtie-Cuffdiff
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| #NOTE: all actions are done with three samples, that have names: 3,4 and 9 | |
| ###IMPROVING FASTQ### | |
| #deleting illumina adapters by https://github.com/vsbuffalo/scythe | |
| ./sickle se -f /home/uploader/flies/assembly5/3_cleaned.fastq -t sanger /home/uploader/flies/assembly5/3.fastq | |
| ./sickle se -f /home/uploader/flies/assembly5/4_cleaned.fastq -t sanger /home/uploader/flies/assembly5/4.fastq | |
| ./sickle se -f /home/uploader/flies/assembly5/9_cleaned.fastq -t sanger /home/uploader/flies/assembly5/9.fastq | |
| #triming fastq by https://github.com/najoshi/sickle |
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