User: jkkbuddika

gravatar for jkkbuddika
jkkbuddika150
Reputation:
150
Status:
Trusted
Location:
Bloomington, USA
Last seen:
2 minutes ago
Joined:
1 month, 3 weeks ago
Email:
j*********@gmail.com

Posts by jkkbuddika

<prev • 27 results • page 1 of 3 • next >
1
vote
1
answer
78
views
1
answers
Comment: C: clusterporfiler enrichGO plot
... I see. That's why giving few more details help. Try the accepted answer in this [thread][1]. Instead of "cyl" in this answer, use ontology (I am not sure how it appears in your dataframe. Check and use the correct form: ontology/ONTOLOGY/Ontology)! That should do it. [1]: https://stackoverflow. ...
written 4 days ago by jkkbuddika150
1
vote
1
answer
78
views
1
answers
Answer: C: clusterporfiler enrichGO plot
... Have you tried doing this? If so posting what you have tried could help. In any case, the [clusterProfiler][1] R package has a detailed user guide that would help you learn how to do anything you want to do. You can make a dot plot simply by using the [dotplot][2] function after performing GO enric ...
written 5 days ago by jkkbuddika150
0
votes
0
answers
82
views
0
answers
Identification of piRNA/siRNAs from small RNA-seq data
... Hi, I am in the process of analyzing a collection of small RNA datasets from flies (Drosophila melanogaster). So far this is what I have done: 1. Trim adaptors using cutadapt and extract 18-30nt long sequences. 2. Align to the Drosophila genome using Bowtie (not Bowtie2): Reads with at least one ...
gene alignment next-gen rna-seq sequencing written 8 days ago by jkkbuddika150
0
votes
1
answer
83
views
1
answers
Comment: C: list of all possible transcripts in ensembl format
... Biomart certainly is the better answer! ...
written 8 days ago by jkkbuddika150
0
votes
1
answer
83
views
1
answers
Comment: C: list of all possible transcripts in ensembl format
... Hi, I think you can gather the information you need from Ensembl [annotations][1]. The following command should make a bed file with transcript information you need. awk '$3 == "transcript"' Homo_sapiens.GRCh38.101.gtf > transcript_info.bed Hope this helps. KB [1]: ftp://ftp.ensembl.org ...
written 8 days ago by jkkbuddika150
0
votes
0
answers
78
views
0
answers
Comment: C: Small RNA data analysis
... That's helpful. Thanks. I ran with default settings and the alignment rate looked pretty good! ...
written 10 days ago by jkkbuddika150
0
votes
0
answers
78
views
0
answers
Comment: C: Small RNA data analysis
... @genomax, I haven't tried bowtie yet. If needed, what parameters would you recommend changing for alignment? I was thinking first running in the default mode and see. ...
written 10 days ago by jkkbuddika150
0
votes
0
answers
78
views
0
answers
Comment: C: Small RNA data analysis
... Awesome. Thanks a lot for all the suggestions. ...
written 10 days ago by jkkbuddika150
0
votes
0
answers
78
views
0
answers
Comment: C: Small RNA data analysis
... Thanks a lot. Will look into that. Do you think Bowtie v1 is the best choice for alignment, over let's say STAR or bowtie2? ...
written 10 days ago by jkkbuddika150
2
votes
0
answers
78
views
0
answers
Small RNA data analysis
... Hi, I am in the process of writing a script to automate small RNA-seq data analysis (18-30nt read length) to identify miRNAs and other types of small RNAs. Based on my reading this is what I came up with. 1. Trim adaptors with Cutadapt. 2. Alignment using Bowtie v1 (old version, not bowtie2). 3. C ...
alignment rna-seq written 10 days ago by jkkbuddika150

Latest awards to jkkbuddika

Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to analyze Illumina RNASeq data
Scholar 6 weeks ago, created an answer that has been accepted. For C: How to count the number of reads aligned to rRNA
Scholar 7 weeks ago, created an answer that has been accepted. For C: How to count the number of reads aligned to rRNA

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1923 users visited in the last hour