Question: RNA seq analysis using STAR+StringTie
0
gravatar for fatima
2.6 years ago by
fatima0
fatima0 wrote:

Hi everybody, I am trying STAR+StringTie. I have done the alignment with STAR and included the option ''--outSAMstrandField intronMotif'' while running STAR to get spliced alignments with XS strand attribute. However, when I run Stringtie I receive this error: input file stringtie cannot be found! Has anybody had the same problem or do you have an idea what I can do???

Thanks in advance. Fatima

rna-seq star stringtie • 3.5k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by fatima0
1

Please show the full command that's producing the error, since you're making a typo somewhere.

ADD REPLYlink written 2.6 years ago by Devon Ryan91k

The answer is STRAIGHT: you're making a typo in the command.

(btw, in english-speaking countries and contexts, "FAG" might assume other meanings that transcend the nickname purpose, FYI)

ADD REPLYlink written 2.6 years ago by Macspider2.9k

Thanks for the replies. The command I used to run STAR:

Path to STAR --runThreadN 20 --genomeDir --outFileNamePrefix --readFilesIn --outSAMtype BAM Unsorted SortedByCoordinate --outWigType bedGraph --outReadsUnmapped Fastx --outSAMstrandField intronMotif

The command I used for stringtie:

path to stringtie/ stringtie D20PMAAligned.sortedByCoord.out.bam -G genes_ensembl_GRCh37_20150717.gtf -o D20_run1.gtf

btw, for STAR I have done 1st pass and 2nd pass, but I only included ''--outSAMstrandField intronMotif'' in the second pass and not the first one! does this cause a problem?

Thank you so much for your help. Fatima

ADD REPLYlink modified 2.6 years ago by genomax70k • written 2.6 years ago by fatima0
1

for STAR I have done 1st pass and 2nd pass, but I only included ''--outSAMstrandField intronMotif'' in the second pass and not the first one! does this cause a problem?

It shouldn't!

path to stringtie/ stringtie D20PMAAligned.sortedByCoord.out.bam -G genes_ensembl_GRCh37_20150717.gtf -o D20_run1.gtf

You have to check that you are in the right directory, because you're not specifying full paths but only filenames. Therefore, you must be inside the directory containing the files. However, I guess that the problem is the space between "/path/to/stringtie" and the word "stringtie".

ADD REPLYlink written 2.6 years ago by Macspider2.9k

Thank you, yes it was a stupid typo!!

ADD REPLYlink written 2.6 years ago by fatima0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1096 users visited in the last hour