Merging .bam files in STAR
Hi there,
I have successfully created an annotated genome index to map my paired-end rna-seq reads and have run:
STAR --runMode alignReads --genomeDir /home/rnaseq/ref/ --outSAMtype BAM SortedByCoordinate --readFilesIn R21_1.fq.gz R21_2.fq.qz --runThreadN 10 --outFileNamePrefix /home/rnaseq/fastq/mapped/R21 --readFilesCommand gunzip
I believe in order to get one .bam file from my paired-end reads I insert both file names with a space between after --readFilesIn. When I run this I receive this error message:
!!!!! WARNING: Could not ls R22_1.fq.qz
EXITING: because of fatal INPUT file error: could not open read file: R22_2.fq.qz
SOLUTION: check that this file exists and has read permision.
I have played around with the files I am using and their order and it seems that no matter what file it is, STAR is unable to read the second file listed. If I run them individually they map successfully so I don't think there is anything wrong with the file itself.
Any help would be really appreciated as this is my first time processing rna-seq data!
• 1,907 views
•
link
written
by
sarah.laverty20 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
t2t RNAseq alignment with STAR
written by eva_u •
-
STAR output
written by Chris •
-
Bam file from STAR
written by Chris •
-
unmapped output of the STAR
written by Wakala •
-
readFilesCommand not working
written by vinishavvenugopal •
-
Alignment loop using STAR
written by lamia_203
-
Strange Error while running STAR.
written by jaidev53ster •
-
STAR alignment error- Segmentation fault (core dumped)
written by EagleEye
-
STAR aligner concordant read
written by 1769mkc
-
STAR aligner fails to produce unmapped file
written by dec986
what is the output of
ls -lah R21_1.fq.gz R21_2.fq.qzI believe it is because my --readFilesCommand gunzip -c command was only unzipping the first file and not the second and therefore the second .fq.gz file was unreadable.
I have now unzipped both files and run the command without --readFilesCommand and it has worked. However, I don't want to have to do this for all of my samples.
Do you know how I can tweak the command to unzip both files?
Try using
--readFilesCommand zcatinstead ofgunzip.In this case, you won't need to unzip your files!
That has worked, thanks so much!