User: Neu

gravatar for Neu
Neu10
Reputation:
10
Status:
New User
Location:
India
Last seen:
1 week, 4 days ago
Joined:
5 years, 2 months ago
Email:
m*****************@gmail.com

Posts by Neu

<prev • 33 results • page 1 of 4 • next >
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Copy number variation study using CNOGpro
... Hi, I want to study copy number variation using *CNOGpro*. Below are my commands. Please help me to resolve the generated errors. library("reutils") library("biofiles") b_file <- reutils::efetch("CP002806", "nuccore", rettype = "gbwithparts", retmode = "text") bk_file < ...
R written 11 days ago by Neu10 • updated 11 days ago by zx87548.2k
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How to fetch gene bank flat file (.gb) in R
... Hello, I need to fetch gene bank flat file of bacteria (Mycobacterium_smegmatis) in R. I have tried using [Biofiles](https://cran.r-project.org/package=biofiles). It's not working and generating the error as below Error in biofiles::gbRecord(mito.path) : 'rcd' must be the path to GenBank ...
R written 12 days ago by Neu10 • updated 12 days ago by WouterDeCoster41k
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Demultiplexing single cell RNA-Seq data
... Hi, I have single cell RNA-Seq data in FASTQ format. I do not have the barcode files. How can I demultiplex it? Please help me with this. Thank you ...
next-gen rna-seq sequencing written 3 months ago by Neu10
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Comment: C: How to merge read count of multiple sample in one fiel to be used for DESeq2 fol
... Hi, I used ablebits-ultimate-suite-excel add-in to do this. Before doing this, I made a single table for the identical columns by merging all the sample result files and then sorted them. ...
written 5 months ago by Neu10
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Comment: C: Help with mRNA region annotation
... Sir, Here mRNA-start means start of the fragment or region of mRNA for which I am interested. What I mean is the fragment of mRNA starting from 2178 to 2215 is a 3UTR/5UTR or CDS. Thank you ...
written 6 months ago by Neu10
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Comment: C: Help with mRNA region annotation
... No Sir, I have just corrected the example. I have a region of mRNA (i.e. that is interacting with another mRNA). I want to know whether it is falling in UTRs and or CDS. ...
written 6 months ago by Neu10
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Help with mRNA region annotation
... Hi, I have mRNA region of interest (mRNA_start-mRNA_end) and I want to find whether it is falling in cds and/or utr(s). The file is as below. How can I do this? mRNA mRNA_start mRNA_end 5utr cds 3utr ENST00000000442.10 2170 2215 UTR5:1-171 CDS:172-1443 UTR3:1444-2215 ...
gene R sequence written 6 months ago by Neu10 • updated 5 months ago by pltbiotech_tkarthi170
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Comment: C: Help with Tophat2 run
... Yes I will surely try that. I am intentionally avoiding star as I can not perform de Novo assembly study with that. Thank you, ...
written 6 months ago by Neu10
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Comment: C: Help with Tophat2 run
... I will be using tophat2-fusion which needs bowtie1 index (https://circexplorer2.readthedocs.io/en/latest/). ...
written 6 months ago by Neu10
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Comment: C: Help with Tophat2 run
... I have 300 GB space available and the PC has 96 GB of RAM. How can I install older version of bowtie2? I am trying it by running `apt-get bowtie2=2.2.1`, but it is not working. The version 2.3.4.1 is getting downloaded with tophat2. Thank you ...
written 6 months ago by Neu10 • updated 3 months ago by h.mon27k

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Popular Question 5 months ago, created a question with more than 1,000 views. For How to exercise RPKM cut-off
Popular Question 5 months ago, created a question with more than 1,000 views. For How to exercise RPKM cut-off

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