Question: Problem mapping mRNA seq data using STAR.
0
gravatar for Seq225
25 days ago by
Seq22550
Seq22550 wrote:

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 alignment assembly • 141 views
ADD COMMENTlink modified 24 days ago by RamRS18k • written 25 days ago by Seq22550

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

ADD REPLYlink written 25 days ago by h.mon20k

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.

ADD REPLYlink written 25 days ago by Seq22550
2

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
ADD REPLYlink modified 25 days ago • written 25 days ago by h.mon20k

Thanks you very much

ADD REPLYlink written 23 days ago by Seq22550
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