polyA anaysis in cDNA data using FLAMAnalysis
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7 weeks ago
bioinfo_ga ▴ 70

Hi ! I am running polyA analysis on cDNA nanopore data using the tool FLAMAnalysis [https://github.com/rajewsky-lab/FLAMAnalysis/]. I am able to run the tool successfully however i am only able to detect polyT tails. I am running the command on raw data without trimming the adaptors. Is there any parameter i need to change?

Thanks.

polyT polyA nanopore cdna • 224 views
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I think providing info (like the command you used and versions of the software) could help others figure out the problem :)

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Software: FLAMAnalysis [https://github.com/rajewsky-lab/FLAMAnalysis/]

Command: python3 FLAMSeqAnalysis.py quantTail -p parameters.yaml

parameters.yaml file look like this: experimentName: "FLAMSeq" # Name of Experiment. This will be prefix for generated analysis files. experiment: rawFastq: "merged.fastq" # Define Path to Input PacBio / Nanopore Reads in fastq format outputDir: "FLAM_seq_Analysis_out" # Define Path to Output dir for writing analysis results. Pipeline will generate of dir is not present. genomeIndexDir: "Test/FLAMseq/Ref/index/" # Define Dir for STARLong Index for Mapping annotationGTF: "Test/FLAMseq/Ref/r.gtf" # GTF File containing gene annotations for assigning reads to genes genomeFasta: "Test/FLAMseq/Ref/r.fasta" # Genome Fasta File containing genome sequence (that the index was generated from)

software: STARlong: "programs/FLAMAnalysis/STARlong/STAR-2.7.11b/bin/Linux_x86_64/STARlong" # Path to STARlong executable featureCounts: "programs/FLAMAnalysis/FeatureCounts/subread-2.0.6-Linux-x86_64/bin/featureCounts" # Path to FeatureCounts executable nThreads: 20

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