Entering edit mode
7.1 years ago
fi1d18 ★ 4.1k
How I could know whether my data sets coming from RNA-seq are strand-specific or not? I emailed the company but they are in Chinese new year and could not help me yet but I should start the analysis.
Just to complete your suggestion with a link =)
Thank you, then I need both bam and bed files? But in UCSC Table Browser there is no such a bed for Arabidopsis, then what to do?
Get the bed from BioMart (Ensembl plant): http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
Make sure the genome build matches.
Thank you, for aligning I used gtf coming from ensembl but there is gff3. no problem?
The main problem is this, I tried to convert my gtf to bed by bedops but some bug that I could not solve then I tried galaxy but in galaxy there is only gff to bed then I used my gtf instead of gff but
Then do you know another solution please?
Looks like you need to provide the path for infer_experiment.py since that does not seem to be in that bin directory.
Thank you but please consider
Try this in case Devon's suggestion did not work
You don't have python installed on this machine? What OS are you using?
python/infer_experiment.pydoes not like that atrocious BED file name. Can you move/copy it to something else and try.
You could ask your sys admins to install the modules or try to install them in your own directory: https://www.seas.upenn.edu/cets/answers/install-python-module.html
It is a bit late in this thread but can't you ask whoever produced this data if they used a "strand-specific" protocol?
I emailed the company but they are in holiday
Not ideal but you could look at the alignments in IGV/Tablet to see if you can see an identifiable pattern in the alignment of reads.
Thank you so much.
In a biostars post I read something about sam flags. Then I saw abundances of 83, 99, 147 and 163 flags of my sam file is the same=1, then might library IS sequenced strand-specific. Anyway I think they will back from holiday Feb 14 and they may reply to my email
Sorry, I installed Python then this is my result
My library was sequenced in strand-specific mode? Sorry if so first or second strand?
No it was not strand-specific. See the explanation here: http://rseqc.sourceforge.net/#infer-experiment-py
Eeek, I had a few missing words in there too! Thanks for adding the link!
Thank you, I aligned but totally on transcriptom and I have
accepted_hits.bamnow. I am in this path:
/usr/data/nfs6/izadi/RSeQC-2.6.3/usr/bin. How can I detect if is strand-specific?