User: connor.geraghty

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Posts by connor.geraghty

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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... These are colon tissue RNA samples from mouse proximal colon. So, some of the transcripts could probably be microbial, but the majority should be mouse. ...
written 16 months ago by connor.geraghty0
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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... Here is the line of code to build the reference index based on the download from NCBI Genome: buildindex(basename="ref_index",reference="GCF_000001635.26_GRCm38.p6_genomic.fna", memory = 48000).  ​By default would the chromosome names be different between the built index from the NCBI, and the inb ...
written 16 months ago by connor.geraghty0
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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... Yes, the reads were mapped to mm10 (GRCm38.p6 to be exact). What is the best way to check if chr names match between reference genome and annotation? ...
written 16 months ago by connor.geraghty0
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Comment: C: featureCounts Returns 0.0% successfully assigned fragments
... Here is the output from fc_PE$stat:  Status X.users.PAS1346.osu9792.testrna.CGL1607_R1.fastq.gz.subread.BAM 1 Assigned 6919 2 Unassigned_Unmapped ...
written 16 months ago by connor.geraghty0
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featureCounts Returns 0.0% successfully assigned fragments
... Hello, I have been working my way through learning Rsubread, and I am stuck on the featureCounts() command. The data maps to the reference genome above 90% for these 5 test samples: NumMapped PropMapped 1 20005679 0.936811 2 15387615 0.909452 3 17158660 0.915605 4 16636690 0.955880 5 ...
rsubread featurecounts written 16 months ago by connor.geraghty0

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