Error with STAR
Hi bioinformaticians,
I am still learning to use STAR and could not pass this error after googling the errors
STAR --runThreadN 8 \
--runMode alignReads \
--genomeDir /home/groups/user/genomeDir \
--readFilesIn /home/groups/user/bulk_RNA-seq/sample1/sample1_1.fq \
--outSAMtype BAM Unsorted
EXITING because of fatal input ERROR: could not open readFilesIn=Read1
Would you please tell what I miss here? For pair end read, path to read 2 will following read 1 with a space or a comma? I appreciate your help!
Update: I could read the fastq file now but still not sure about the input for the pair end read.
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Hi! Separate
read1andread2files with a space, see STAR manual here.Thank you! The other manual I read use [] for read 2 which made me confused.
https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf
[]refers to an optional parameter, not a literal[]. Command line tools will never ask for[]or()or{}as these are all shell metacharacters.What the manual is saying is that you can give a single FQ file if the FQ is Single Ended and 2 FQs in a space separated manner if you have PE FQs.
Thank you for the knowledge! If I only provide read 1, STAR creates a lot of files. If I provide both reads, there are fewer files created by STAR. Would you give a comment on this?
Results or temporary files? What about directories (Look for directory name patterns:
*_STARgenome,*_STARtmp,*_STARpass1)I ran again with only read 1 and the number of files created is the same as providing both reads. What happened if I use only the output of read 1 for the next step with featurecounts?
I have these files:
testAligned.out.bam
testLog.final.out
testLog.out
testLog.progress.out
testSJ.out.tab but not as you wrote in red.
I'm using code formatting to present content better. See how it looks when I format your content:
I ran again with only read 1 and the number of files created is the same as providing both reads. What happened if I use only the output of read 1 for the next step with featurecounts?
I have these files:
but not as you wrote in red.
Thank you for your reply. I thought it is the output so I didn't put in code formatting. Is that the post you mean to answer my question about using SE and PE?
mapping PE or SE?
Anything you're copy pasting from a terminal/console is better off in code formatting. If it's text generated by a program, (think output or error produced by a command), code formatting will format it best.
There might be multiple posts on this forum and elsewhere addressing SE vs PE mapping - all I'm saying is that it's a different topic and should not be discussed in this thread.
Your question is now about the difference between using SE and PE reads in RNAseq quantification, which is sufficiently different from your top level question to warrant being its own post (after searching the forum for existing posts that already address this question)
Hi Ram,
I ran again and got 10 files output instead of 5 for providing only read 1:
Would you have a comment on this?
All the
.outfiles are logs, so exclude the from the outputs category. You only have BAM and the SJ tab as the actual output.Also, correct me if I'm wrong but this looks like a cumulative set of files. As in, you ran again and got 5 more files so with the 5 previous files, that makes 10. I am guessing this because one of your runs has the prefix
testand the other has the prefixtestsampleand the rest of the file name components are the same:I remember I made a temp folder to contain the output files but let me run again to check. Thank you.