安裝中文字典英文字典辭典工具!
安裝中文字典英文字典辭典工具!
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- Rseqqc And Rna-Seqqc - Quality Control Software For Rna-Seq Data
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq specific modules” investigate sequencing saturation status of both splicing
- RSeQC - geneBody_coverage. py - Cannot get coverage signal from . . . bam
I have successfully installed RSeQC and python -c ‘from qcmodule import SAM’ runs without error I have tried the following command on a sorted and indexed bam file output from STAR aligner and indexed with samtools geneBody_coverage py -r hg38 HouseKeepingGenes bed -i Aligned sortedByCoord out bam -o coverage
- Good QC Package (RSeQC or alternative) for Salmon mapping . . .
RSeQC seems like a good tool for this, able to generate many metrics about the mapping Unfortunately, it seems like RSeQC only takes BAM SAM files, whereas I have quant sf and other output files from Salmon
- Infering strand specificity of bam files using rseqc? - Biostar: S
I have run infer_experiment py of rseqc package to identify the strandedness of the aligned bam file so that I can feed -s option of featureCounts I used following command to generate the output: infer_experiment py -r hg38 bed -i xxy2 sort bam
- RSeQC: Problems calling geneBody_coverage. py on a directory - biostars
I'd like to use the geneBody_coverage py script in RseQC to analyze some bam files Because I have a lot of bam files, I'd like to be able to do this in a batch
- gene body coverage with RSeqQC - Biostar: S
I downloaded the directory directly off the site (RSeQC-5 0 1) however it's failing for qcmodule import from qcmodule import getBamFiles ModuleNotFoundError: No module named 'qcmodule'
- RSeQC - does it make sense to run it on the genome BAM when alignment . . .
In my opinion, if you load up a few of you BAM files into IGV within a few minutes of visual inspection you can understand more about its properties than with RSeQC You can tell the coverages, evenness, and replication quality Look at untranslated regions, splice junctions - many properties will be evident
- Rseqc infer_experiment. py: 0 usable reads sampled and unknown data type
I was trying to use rseqc to check strandedness of my fastq files It requires two inputs: an aligned SAM file and a BED file To create the SAM file, I aligned my reads using bowtie2
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