How to create SJ.out.tab files from bam files
I downloaded thousands of RNA-Seq bam files aligned using STAR in 2-pass mode. For some parts of my analysis, I need SJ.out.tab files for each sample that are typically generated during STAR alignment process. But I don't have these files because I didn't do the alignment by myself and I don't have the original FASTQ files. Is there any way to create SJ.out.tab files from bam files?
• 2,105 views
•
link
written
by
freeustand •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Nextflow STAR alignment process only aligning one fastq file when 6 are being passed in
written by smarcotte11 •
-
Alignment prior to passing SAM/BAM to DEXSeq
written by wiscoyogi •
-
STAR mapping two pass mode for multiple samples with split steps or one step ?
written by octpus616 •
-
STAR mapping pipeline with 2-pass for multiple samples?
written by Rajesh Detroja
-
STAR two -pass mode - lower alignment rate than one pass mode?
written by Biogeek
-
Realign Aligned.sortedByCoord.out.bam to Aligned.toTranscriptome.out.bam for RSEM input
written by mkvalluru •
-
Generating a gene expression matrix from Picard *duplicates_marked.bam file
written by halo22
-
Should I use a bad/ mediocre gene model as input for STAR RNA-seq alignment?
written by William
-
Multiple RNAseq Library to SNP Call using GATK
written by Bioinfonext
-
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
written by kirannbishwa01
STAR has a mailing list and Alex Dobin (STAR's author) is very responsive, you should try asking there. But I am afraid you will have to extract the reads from the bam file and align again.