Search Results for "cufflinks"

rna_test.sh is a shell script to run GATK best practice for variant-calling in RNAseq. It uses STAR2.5 for alignment, HaplotypeCaller to call variants, and Annovar to annotate. It also employs STAR-Fusion, Cufflinks and Stringtie FPKM, HTSeq_count and BAM-readcount. Notice: STAR_gene_read and HTSeq_count are added. exac03nontcga is added. STAR-Fusion is added. Stringtie is added. Disable BQSR (-skb) opteion is added. New avsnp(150) is updated. use -dcov in SplitNCigarReads added. Mutlithreading for dbsnp annotation, Haplotypecaller, and bamreadcount more efficient. ...

...PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results

...The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk

This code is a solution to collapsing duplicate FPKMs for a gene. Problem/Issue: In the cufflinks output files *_genes.expr (which reports the gene-level coordinates and expression values), sometimes I get more than one row for the same gene? It's like in some cases the FPKM values from the transcripts corresponding to the same gene do not get summed, although the transcripts are assigned to the same gene. Reasons and Solution: The multiple FPKM problem occurs when genes have transcripts that do not overlap with any other transcripts in the gene. ...

The purpose of DressUp is to create an end-to-end RNA seq pipeline in which all of the steps of analyzing data from an Illumina sequencer is done in one step in an HPC environment. RNA seq programs included are TopHat, CuffLinks, CuffDiff, CuffMerge, FastQC, and trimming using the FastX toolkit. DressUp facilitates RNA seq programs by streamlining various packages into a single script. That script executes the RNA seq programs on a batch cluster system. Upon execution of the script, jobs are submitted to the cluster depending on attributes set up in the configuration file. ...

A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.