User: realnewbie

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realnewbie20
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3 years, 8 months ago
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Posts by realnewbie

<prev • 34 results • page 1 of 4 • next >
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likelihood of number of consecutive Ns in miRNA sequence
... Hi, Dear community, I have a very interesting question. I am planning to count the number of sequences with greater than some consecutive number of nucletodies (i.e number of sequences with >=5 Gs) as empty product. Do you have any idea about the likelihood of consecutive Ns in miRNA sequences? ...
mirna likelihood written 7 months ago by realnewbie20 • updated 7 months ago by Jeremy Leipzig19k
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Comment: C: mirdeep2 step-by-step tutorial
... Hi, In case someone still needs it, here is the tutorial I found s/he can try (adapted from mirdeep2 tutorial) in [this website][1]. [1]: http://rsgturkey.com/en/mirdeep2-mirna-sequencing-analysis-example-run-by-using-ubuntu-terminal/ ...
written 8 months ago by realnewbie20
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Comment: C: miRDeep2 whitespaces error
... I have encountered to the same problem for this code: dos2unix GRCh38_primary_assembly_genomeCopy.fasta I run dos2unix.However, I could not solve it via dos2unix. This is the error code I received: > dos2unix: Failed to change the owner and group of temporary output file ./d2utmpVftysK: Op ...
written 8 months ago by realnewbie20
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Comment: C: Possible reasons mapping percentage abysmally low for miRNA reads?
... Hi, I was doing the same analysis and I got 0, 0, 0.03 and 0.03 mapped reads. None of the reads were mapped at all! I wonder whether bbmap.sh instead of bowtie increased your mapping quality or not. Thanks! ...
written 8 months ago by realnewbie20
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Comment: C: miRDeep2.pl cannot recognize reference fasta file
... Thanks a lot! I realized that in the mapper we are using bowtie indexed reference genome, however, in the mirdeep.pl step, we need to use not indexed-original fasta file. The old tutorial was a little bit confusing regarding this issue. New tutorial is more helpful. Best, ...
written 8 months ago by realnewbie20
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Comment: C: miRDeep2.pl cannot recognize reference fasta file
... Tutorial page sucks. It was not useful at all. It was impossible to download the relevant files properly without conda install. ...
written 8 months ago by realnewbie20
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Comment: C: miRDeep2.pl cannot recognize reference fasta file
... Yes, they are in the same directory. By the way, thanks a lot for your quick response to help. ...
written 8 months ago by realnewbie20
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Comment: C: miRDeep2.pl cannot recognize reference fasta file
... What is "plain fasta" file? I have been using this: **Homo_sapiens.GRCh37.dna.primary_assembly.fa**. In tutorial, it says we need to index the fasta file first. > For novel miRNA prediction we need to map the reads against a reference database which has to be indexed by bowtie 1. For this we t ...
written 8 months ago by realnewbie20
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miRDeep2.pl cannot recognize reference fasta file
... Hi, I have been trying to run mirdeep2 for a while. However, the tool cannot recognize bowtie-indexed reference genome at mirdeep2.pl step. It gives the same error: "refence.fa is not a fasta file". However it runs same file for mapping. When it comes to mirdeep2.pl, it could not. I could not unders ...
fa mirna sequencing mirdeep2 mirdeep2.pl mirna written 8 months ago by realnewbie20
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Comment: C: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
... The code above was working two days ago, but did not work yesterday. Here is the thing, I guess, one of the packages I have downloaded before GenomicFeatures prevented the code above to work properly (although there were no warning, package masking). Where do I know this from? Simple, today the co ...
written 24 months ago by realnewbie20

Latest awards to realnewbie

Popular Question 6 months ago, created a question with more than 1,000 views. For NextSeq 500 RNA-Seq results
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Popular Question 14 months ago, created a question with more than 1,000 views. For Changes log2FC values of DESeq2
Popular Question 22 months ago, created a question with more than 1,000 views. For Changes log2FC values of DESeq2
Popular Question 2.8 years ago, created a question with more than 1,000 views. For TCGA data(RPKM) differential gene expression

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