STAR alignment issue
Hello I am using STAR on my computer with 32gb RAM, I successfully made Index , my index directory (STARindex) seems to have all the files. But my alignment is done in 2 minutes and I am getting BAM file only 3kb. Can anyone suggest where I am going wrong , thank you
STAR --runMode alignReads \
–-runThreadN 6 \
--genomeDir STARindex \
--sjdbGTFtagExonParentTranscript Parent Hg19.gtf \
--readFilesIn ERR420386_1.fastq ERR420386_2.fastq \
--outSAMtype BAM Unsorted
This is the response I get
May 17 00:27:31 ..... started STAR run May 17 00:27:31 ..... loading genome May 17 00:29:24 ..... started mapping May 17 00:29:24 ..... finished mapping May 17 00:29:26 ..... finished successfully
Please help
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srinivasa rao •
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srinivasa rao •
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How does your Hg19.gtf look like?
Hg19.gtf looks good, this is the same file I used for my index , 828,000kb , this file doesn't need to be in Index directory correct ?
It looks like STAR ran correctly, try without this parameter:
No luck , I tried without --sjdbGTFtagExonParentTranscript Parent Hg19.gtf \ , I see 0 reads aligned somewhere I am missing not able to figure it out
Interesting, everything looks ok, try HISAT2, if you get the same result maybe the problem is your input files, probably your reads do not correspond to your genome reference.