Problem mapping mRNA seq data using STAR.

Question

[Seq225]

I am running STAR on paired end reads:**

star --runThreadN 50 --genomeDir index --readFilesIn ASS_1_1.fq.gz ASS__1_2.fq.gz --outFileNamePrefix ASS.mapped.sam --readFilesCommand gzcat

Sep 21 16:20:32 ..... started STAR run
Sep 21 16:20:33 ..... loading genome
Sep 21 16:20:39 ..... started mapping

EXITING because of FATAL ERROR in reads input: short read sequence line: 0
Read Name=@NB501259:103:HNTJLBGX2:1:21310:2440:4630
Read Sequence====
DEF_readNameLengthMax=50000
DEF_readSeqLengthMax=650

Sep 21 16:21:53 ...... FATAL ERROR, exiting
Segmentation fault: 11

I have cut my reads by cutadapt. Is there any option in STAR to get this problem around? Or, I have to do something with the cutadapt now?

Thanks.

[h.mon]

After trimming your reads, did you run then through FsatQC? Check their length distribution.

[Seq225]

There are some 0 nt reads. I am sure about that. STAR (or any other aligner probably) had problem working on 0 nt reads. I am asking if they have resolved that issue? Or I have to delete those reads from my file.

[h.mon]

You have to delete those reads from your file, but do this carefully, to keep the forward and reverse reads properly paired. One option reformat.sh from BBTools / BBMap package:

reformat.sh in1=R1.fastq in2=R2.fastq out1 R1ml.fastq out2=R2ml.fastq minlen=25

[Seq225]

Thanks you very much

[lkianmehr]

excuse me, minlen option is constant or may I change it? what it depends?

[Seq225]

I think you can change it. I guess the default is 60. Please check their manual.