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RBL-19

Wilfried Guiblet 2026-02-16

Tailer Analysis

module load python
#pip install jla-tailer
Tailer -a references/gencode.v49.annotation.gtf rawfiles/17.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/17multi.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/99.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/99multi.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/ctrl.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/c_multi.bam

mv rawfiles/*_tail.csv Tailer/gencode_genes/

export NXF_SINGULARITY_CACHEDIR=$PWD/.singularity export SINGULARITY_CACHEDIR=$PWD/.singularity

singularity pull bed2gtf.sif docker://wilfriedguiblet/bed2gtf:v0.1 singularity shell -B $(pwd)/:/data2/ bed2gtf.sif

bed2gtf -b hg38-tRNAs.bed -o hg38-tRNAs.gtf –no-gene

Appends gene_name “<gene_id_value>” at the end of the line:

sed -E ‘s/(gene_id “([^"]+)”;)/\1 gene_name “\2”/’ hg38-tRNAs.gtf > hg38-tRNAs.withnames.gtf

switch to exon

vim /home/guibletwm/.local/lib/python3.10/site-packages/Tailer/TailerFunctions.py

module load python
#pip install jla-tailer
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/17.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/17multi.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/99.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/99multi.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/ctrl.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/c_multi.bam


#c_multi is too big

samtools view -s 0.25 -b rawfiles/c_multi.bam > rawfiles/c_multi.subset.bam
samtools index rawfiles/c_multi.subset.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/c_multi.subset.bam
mv rawfiles/c_multi.subset_tail.csv Tailer/tRNAs/