ERROR in RNA STAR

[Deepa Ramasamy]

Hello,

I am trying to align the RNA seq data of 75bp SE reads which is of RIP sequencing reads. I am ended up with the ERROR stating "EXITING because of FATAL ERROR in reads input: short read sequence line: 1
Read Name=@NB552097:347:HTGY3BGXH:1:11112:8194:11887
Read Sequence====
DEF_readNameLengthMax=50000
DEF_readSeqLengthMax=650"

And these are my codes

STAR --runThreadN 22 --genomeDir /illumina/data/m6A/fasta/STAR_index/ --readFilesIn HT29_MeRIP_CA.fastq --outFileNamePrefix HT29_MeRIP_STAR --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within

Also, I have generate genome index using --sjdbOverhang 74.

Could you please help me in sorting the issue?

Thank you.

Regards,

Deepa. R

[Alexander Dobin]

Hi Deepa,

it looks like there is an issue with formatting of the FASTQ file. Please check first the line that follows @NB552097:347:HTGY3BGXH:1:11112:8194:11887

[Manjunatha B K]

Try to reduce the number of threads, let's say 16 or something.

STAR throws errors with higher threads sometimes.

Thank you.

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