- R-SAP: High-throughput RNA-Seq analysis pipeline (Pubmed): An automated mutli-threaded computational pipeline to analyze and detect novel transcriptional events from next generation RNA-Seq datasets
- C.elegans data (Pubmed):Includes supplemental data from Ganko et al 2003 and up-to-date Wormbase Browser retrotransposon location files
- LTR_STRUC (Pubmed): Application from McCarthy and McDonald 2003 that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits
Other sequencing data analysis programs from our lab:
| Program | Description |
| CountSplicedReads | Counts the number of spliced reads (or splice junction mapping reads) in a given RNA-Seq reads genomic alignment bam file. |
| DetermineFastqQualityEncoding | Determines quality value encoding format in a given fastq file. |
| FastqPairedEndValidator | Validates order of paired-end reads in given fastq files. |
| AddPairedEndSuffix | Adds \1 and \2 suffix (tags) to the first (left) and second (right) pairs of paired-end read names respectively in given fastq files. |
| FqToSamPicard | Converts paired-end fastq files to a merged and sorted (on read name) SAM file. |
| UnmappedSamToFastq | Fixes the order of appearance of paired-end reads in fastq files using a merged SAM files and also separates unpaired reads. |
Other resources:
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- How to fix the order of appearance of mates of paired-end sequencing reads in fastq files?
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- How to improve RNA-Seq alignment using TopHat? (2013)