Load velocyto ml velocyto velocyto-team/velocyto.py#130 CB Z Cell identifier UB appears to be UMI tag # Try downloading an ENCODE RNAseq BAM file: GM12878, RNASeq (GINGERAS), Total Long, Whole-cell http://genome.crg.es/encode_RNA_dashboard/hg19/ Bio rep 1 wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/releaseLatest/wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep1.bam Bio rep 2 wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/releaseLatest/wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep2.bam # Add CB, UB tags python3 add_cb_ub_tags.py wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep1.bam python3 add_cb_ub_tags.py wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep2.bam # Run velocyto velocyto run -U wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep1_withtags.bam ~/dat/ensembl/gtf/Homo_sapiens.GRCh37.87.chr.gtf.gz samtools sort -l 7 -m 512M -t CB -O BAM -@ 8 -o /scratch/bclab/aramu/analysis/velocity/2019-01-02-test-velocyto/wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep1_withtags_sorted.bam /scratch/bclab/aramu/analysis/velocity/2019-01-02-test-velocyto/wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep1_withtags.bam samtools view -bh wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep2_withtags.sam | samtools sort -l 7 -m 512M -t CB -O BAM -@ 8 -o /scratch/bclab/aramu/analysis/velocity/2019-01-02-test-velocyto/wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep2_withtags_sorted.bam mv wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep1_withtags_sorted.bam Rep1.bam mv cellsorted_wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep1_withtags_sorted.bam cellsorted_Rep1.bam mv wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep2_withtags_sorted.bam Rep2.bam mv cellsorted_wgEncodeCshlLongRnaSeqGm12878CellTotalAlnRep2_withtags_sorted.bam cellsorted_Rep2.bam K562 wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/releaseLatest/wgEncodeCshlLongRnaSeqK562CellTotalAlnRep1.bam wget --no-check-certificate http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/releaseLatest/wgEncodeCshlLongRnaSeqK562CellTotalAlnRep2.bam mv wgEncodeCshlLongRnaSeqK562CellTotalAlnRep1.bam K562_Rep1.bam mv wgEncodeCshlLongRnaSeqK562CellTotalAlnRep2.bam K562_Rep2.bam python3 add_cb_ub_tags.py K562_Rep1.bam python3 add_cb_ub_tags.py K562_Rep2.bam # I might have overwritten the K562 Rep2 while combining the loom files :( python3 combine_loom.py velocyto/Rep1_6T8PI.loom velocyto/Rep2_E9TS0.loom velocyto/K562_Rep1_withtags_TXR6K.loom velocyto/K562_Rep2_withtags_LCBND.loom combined_4samples_v2.loom cp velocyto/K562_Rep2_withtags_LCBND.loom velocyto/combined_4samples.loom python3 combine_loom.py velocyto/Rep1_6T8PI.loom velocyto/Rep2_E9TS0.loom velocyto/K562_Rep1_withtags_TXR6K.loom velocyto/K562_Rep2_withtags_OWVYP.loom combined_4samples_v2.loom