CODEWITHSUNDEEP
linuxcommand-linebioinformaticssequencing
user12006540
user12006540

Reputation: 15

STAR mapping is creating empty BAM file

I'm trying to run STAR but I am getting an empty BAM file. Does anyone know why this is happening and how to fix it?

iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN \
> --annotation homo_sapiens.88.gtf.gz 
#for context, mapstar needs the following arguments reads, genome_index, out_dir

iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN --annotation homo_sapiens.88.gtf.gz
Input parameters for function 'map_reads' in iCount.externals.star
    reads: demultiplexed/demux_NNNGGCGNN.fastq.gz
    genome_index: hs88
    out_dir: mapping_NNNGGCGNN
    annotation: homo_sapiens.88.gtf.gz
    multimax: 10
    mismatches: 2
    threads: 1
    genome_load: False
Mapping reads from demultiplexed/demux_NNNGGCGNN.fastq.gz
Nov 02 20:23:11 ..... started STAR run
Nov 02 20:23:11 ..... loading genome
Nov 02 20:23:12 ..... processing annotations GTF
Nov 02 20:23:32 ..... inserting junctions into the genome indices
Nov 02 20:23:34 ..... started mapping
Done.

Upvotes: 0

Views: 144

Answers (1)

gecko007
gecko007

Reputation: 79

I solved the issue by replacing --readFilesCommand zcat by --readFilesCommand gunzip -c

Upvotes: 0

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