User: noahhelton98

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Posts by noahhelton98

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Answer: A: RNAseq splicing tools
... Yes just input the path to the merged gtf file: rmats.py --gtf /path/to/merged.gtf They have answered this in their FAQs as well http://rnaseq-mats.sourceforge.net/rmats3.2.4/faq.html ...
written 8 days ago by noahhelton980
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Comment: C: Issue installing rmats using conda
... I've tried both ways and get the same results. ...
written 5 weeks ago by noahhelton980
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Comment: C: Issue installing rmats using conda
... Do you run on Mac? I tried to do the build step and got this error: > > rm: *.so: No such file or directory rm: *.so.*: No such file or directory cd rMATS_C; make; cd lbfgs_scipy && make gfortran -c -O2 -c > -o lbfgsb.o lbfgsb.f gfortran -c -O2 -c -o linpack.o linpack.f gfortran ...
written 5 weeks ago by noahhelton980
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Comment: C: Issue installing rmats using conda
... Is there any issues when trying to run rmats on Mac by chance? I have tried this a few different ways and I just can't seem to get it to work. ...
written 5 weeks ago by noahhelton980
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Issue installing rmats using conda
... I am trying to install rmats using conda install -c bioconda rmats and I keep getting this issue **UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - rmats -> python[versi ...
rmats splicing conda rna-seq written 5 weeks ago by noahhelton980 • updated 5 weeks ago by benformatics2.0k
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Answer: A: compare expression for 1 gene between more than 2 samples
... If you used the same control for each of the different samples, then any measure should be fine. Differential gene expression is relative, so when comparing expressing across multiple samples you can compare their relative change to the control and use that when talking about the data. Log2FC should ...
written 7 weeks ago by noahhelton980
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Comment: C: Running a hisat2 loop, samtools view and sort using python
... Thanks so much, I am trying to run this code, but for some reason it keeps saying their is no such directory as _1.fastq.gz and "gzip: can't stat: _2.fastq.gz (_2.fastq.gz.gz)". For my loop I had put for i in trimmed_reads/*_1.fastq.gz do ... what you said had in the code my file names ...
written 7 weeks ago by noahhelton980

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