User: oolongoni
oolongoni • 10
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Posts by oolongoni
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... Thanks for your input! I can try changing the index directory name from `/share/projects/RNASeq/data/reference/GRCh38/grch38_tran/` to `/share/projects/RNASeq/data/reference/GRCh38/genome_tran` after the job is finished running. ...
written 3.4 years ago by
oolongoni • 10
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6.3k
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... Thank you sir! I guess it makes sense now. I wonder why renaming the `*ht2` index files did not work. ...
written 3.4 years ago by
oolongoni • 10
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6 follow
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... First time trying out HISAT2 and I'm having a problem here, even with the pre-made indices for GRCH38.
$ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-0308 ...
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... Solved it! It was erroneously naming the cdfname. Doh!
raw.data = ReadAffy(verbose=TRUE, filenames=cels, cdfname="u133aaofav2hsentrezg") ## not "u133aaofav2hsentrezgcdf" ...
written 3.9 years ago by
oolongoni • 10
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... Hello,
I am trying to analyze the GSE24759 dataset using the raw CEL files. I was hoping to use gcrma to process the data but ran into complications downloading the custom CDF "U133AAofAv2_Hs_ENTREZG" from Brainarray. http://brainarray.mbni.med.umich.edu/bioc/
I found a tutorial here (https://githu ...
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9 months ago,
created a question with more than 5,000 views.
For Could not locate a HISAT2 index to basename
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2.4 years ago,
created a question with more than 1,000 views.
For Could not locate a HISAT2 index to basename
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Could not locate a HISAT2 index to basename
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