README.md
In theron-palmer/splicemute: splicemute
splicemutr is a tool for evaluating how individual splice junctions affect coding transcripts from RNAseq data.
Software USED
STAR: 2.7.3a
R: 4.0.2
STAR Alignment of RNAseq data
The fastq files were aligned using the following command:
STAR --genomeDir $GENOME_DIR --readFilesIn ${fastq1} ${fastq2} --twopassMode Basic --outSAMstrandField intronMotif --outFileNamePrefix $outprefix --runThreadN 6 --readFilesCommand zcat --outSAMtype BAM Unsorted
Converting STAR SJ.out.tab files to splicemutr .junc files
STAR outputs high confidence junction files as well as BAM files. These junction files must be converted to filetypes appropriate for the next steps in the splicemutr pipeline. This is done in the following way, using the associated script file:
splicemute/scripts/STAR_to_leaf.R -o $OUT -s $STAR_FILE
theron-palmer/splicemute documentation built on Jan. 8, 2022, 10:36 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
splicemutr is a tool for evaluating how individual splice junctions affect coding transcripts from RNAseq data.
Software USED
STAR: 2.7.3a R: 4.0.2
STAR Alignment of RNAseq data
The fastq files were aligned using the following command:
STAR --genomeDir $GENOME_DIR --readFilesIn ${fastq1} ${fastq2} --twopassMode Basic --outSAMstrandField intronMotif --outFileNamePrefix $outprefix --runThreadN 6 --readFilesCommand zcat --outSAMtype BAM Unsorted
Converting STAR SJ.out.tab files to splicemutr .junc files
STAR outputs high confidence junction files as well as BAM files. These junction files must be converted to filetypes appropriate for the next steps in the splicemutr pipeline. This is done in the following way, using the associated script file:
splicemute/scripts/STAR_to_leaf.R -o $OUT -s $STAR_FILE
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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