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01_trim_galore.bash
02_trinity.bash
03_gmap.bash
04_cuffmerge.sh
05_star_index.sh
06_star_map.bash
07_samtools_view.bash
08_novosort.bash
09_samtools_cat.bash
10_rsem_index.sh
11_rsem_quantify.bash
12_rsem_makeGenomeLevelBam.bash
13_bedtools_makeExonLevelCounts.bash
README.md

README.md

Identification and quantification of non-coding RNAs

This repository provides bash scripts used in Moradi Marjaneh et al. (Genome Biology, 2020) to identify and quantify ncRNAs including:

  1. trimming the sequencing reads with trim_galore
  2. de novo assembly with Trinity
  3. mapping back the de novo assemblies against hg19 reference genome with gmap
  4. merging assemblies with cuffmerge
  5. STAR indexing
  6. mapping the sequencing reads against the merged assembly with STAR
  7. filtering for paired mapped reads with samtools view
  8. sorting with novosort
  9. merging sorted bam files for each library with samtools cat
  10. indexing with rsem-prepare-reference
  11. quantification (gene and isoform level) with rsem-calculate-expression
  12. making genome level bam files with rsem-calculate-expression
  13. exon level quantification with samtools view and coverageBed

References

Moradi Marjaneh M, Beesley J, O’Mara TA, Mukhopadhyay P, Koufariotis LT, Kazakoff S, et al. Non-coding RNAs underlie genetic predisposition to breast cancer. Genome Biology. 2020; 21(1):7. (PMID: 31910864)

Bartonicek N, Clark MB, Quek XC, Torpy JR, Pritchard AL, Maag JLV, et al. Intergenic disease-associated regions are abundant in novel transcripts. Genome Biology. 2017; 18:241. (PMID: 29284497)

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