STAR alignment issue
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11 weeks ago

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

STAR RNAseq • 328 views
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How does your Hg19.gtf look like?

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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 ?

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It looks like STAR ran correctly, try without this parameter:

--sjdbGTFtagExonParentTranscript Parent Hg19.gtf \
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No luck , I tried without --sjdbGTFtagExonParentTranscript Parent Hg19.gtf \ , I see 0 reads aligned somewhere I am missing not able to figure it out

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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.

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