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Problem mapping mRNA seq data using STAR.

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.

rna-seq assembly alignment
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updated by Biostar Biostar • written by Seq225 Seq225

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

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written by h.mon h.mon

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.

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written by Seq225 Seq225

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
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written by h.mon h.mon

Thanks you very much

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written by Seq225 Seq225

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

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written by lkianmehr lkianmehr

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

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written by Seq225 Seq225

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