For loop rna sequencing alignment
Hey guys... I am trying to do a for loop to align my samples to a reference file in terminal.....can someone help me...I am getting this error:
EXITING because of fatal input ERROR: could not open readFilesIn=Read1
This is the code I put in
for f1 in `cat MatchedFastqList.txt` ;do SAMPLE=$(echo ${f1}| sed "s/_1\.fastq\//"); echo ${SAMPLE}.bam; echo
STAR --runThreadN 16 --genomeDir /folder/to/project/ncbi-genomes-2022-09-19/
GCF_000001405.40_GRCh38.p14_genomic.fna --sjdbGTFfile /folder/to/projects/GCF_000001405.40_GRCh38.p14_genomic.gtf
--readFilesIn ${f1} --outReadsUnmapped Fastx ; done
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Aligning fastq files using STAR
written by kcarey •
-
For loop for aligning multiple paired end fastq files
written by kcarey •
-
Having trouble Aligning paired end reads with STAR
written by kcarey •
-
STAR mapping with genomeLoad issue bash script
written by luckysardar171 •
-
For loop RNA Sequencing alignment
written by kcarey •
-
star --readFilesIn error when using unmapped.out.mate1/2 files
written by kokoko •
-
ERROR In aligmnet of RNA_seq data using STAR aligner_updated
written by akhan •
-
ERROR In aligmnet of RNA_seq data using STAR aligner
written by akhan •
-
Error while running STAR aligner
written by XBria
-
STAR aligner fails to produce unmapped file
written by dec986
not an answer but : you'd better use a workflow manager like snakemake or nextflow.
what is "this error" ?
Thank you for your feedback. I am self-taught learning coding. What is a workflow manager? Is it super beneficial for longer pipelines?
definitively
https://pubmed.ncbi.nlm.nih.gov/28398311/
https://pubmed.ncbi.nlm.nih.gov/35037206/
404: Error Not Found(Now seriously, you forgot to copy the error ;) )
So far the only thing that I can see is that the
donein the end of the loop is missing.Sorry, I was rushing I got this error
It also is not going down the list to each file...
Can you copy-paste the content of
MatchedFastqList.txt?It contacts samples that are set up like this "Sample345.fastq" and its all listed