├── README.md ├── job_scripts ├── README.md ├── fastqc.sh ├── rcorector.sh └── rm_rcorrector_unfixable.sh ├── test ├── fastqc_data_r1.txt ├── fastqc_data_r1_nooverrep.txt ├── fastqc_data_r2.txt ├── fastqc_data_r2_nooverrep.txt ├── test_R1_adaptor-trimmed.fq.gz └── test_R2_adaptor-trimmed.fq.gz └── utilities ├── FilterListConverBam2Fastq.py ├── FilterUncorrectabledPEfastq.py ├── README.md ├── RemoveFastqcOverrepSequenceReads.py └── RepairSRAHeadersForTrinity.py /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/README.md -------------------------------------------------------------------------------- /job_scripts/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/job_scripts/README.md -------------------------------------------------------------------------------- /job_scripts/fastqc.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/job_scripts/fastqc.sh -------------------------------------------------------------------------------- /job_scripts/rcorector.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/job_scripts/rcorector.sh -------------------------------------------------------------------------------- /job_scripts/rm_rcorrector_unfixable.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/job_scripts/rm_rcorrector_unfixable.sh -------------------------------------------------------------------------------- /test/fastqc_data_r1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/test/fastqc_data_r1.txt -------------------------------------------------------------------------------- /test/fastqc_data_r1_nooverrep.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/test/fastqc_data_r1_nooverrep.txt -------------------------------------------------------------------------------- /test/fastqc_data_r2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/test/fastqc_data_r2.txt -------------------------------------------------------------------------------- /test/fastqc_data_r2_nooverrep.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/test/fastqc_data_r2_nooverrep.txt -------------------------------------------------------------------------------- /test/test_R1_adaptor-trimmed.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/test/test_R1_adaptor-trimmed.fq.gz -------------------------------------------------------------------------------- /test/test_R2_adaptor-trimmed.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/test/test_R2_adaptor-trimmed.fq.gz -------------------------------------------------------------------------------- /utilities/FilterListConverBam2Fastq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/utilities/FilterListConverBam2Fastq.py -------------------------------------------------------------------------------- /utilities/FilterUncorrectabledPEfastq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/utilities/FilterUncorrectabledPEfastq.py -------------------------------------------------------------------------------- /utilities/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/utilities/README.md -------------------------------------------------------------------------------- /utilities/RemoveFastqcOverrepSequenceReads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/utilities/RemoveFastqcOverrepSequenceReads.py -------------------------------------------------------------------------------- /utilities/RepairSRAHeadersForTrinity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/harvardinformatics/TranscriptomeAssemblyTools/HEAD/utilities/RepairSRAHeadersForTrinity.py --------------------------------------------------------------------------------