User: ashish

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ashish320
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Posts by ashish

<prev • 124 results • page 1 of 13 • next >
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Answer: A: Heatmap value gradient
... You need to change atleast two things here 1. write `qplot` instead of `ggplot`. 2. add `scale_fill_manual(values=c("3"="green", "1"="red"))` at the end of your command It should look like this: qplot(data=Good1_Poor3, x=sample_id, y=Gene, fill=factor(response) ...
written 4 weeks ago by ashish320
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Comment: C: Need to create a small artificial SRA file for unit testing
... You can simulate random reads from a genome using [randomreads.sh][1] from bbtools. The resulting reads can be converted to .sra using sra-toolkit. [1]: http://seqanswers.com/forums/showthread.php?t=58221 ...
written 4 weeks ago by ashish320
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Comment: C: How to extract 3'UTR regions
... Use [bedtools complement][1] It will give you all the regions not represented in your gff file. You can then use it extract all the "non-CDS" regions from your genome but to identify UTRs in those regions will take more downstream steps. How did you end up with a gff file containing only CDS coordin ...
written 4 weeks ago by ashish320
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Comment: C: How to extract 3'UTR regions
... It would help if you post `head` of the fasta and gff files and also mention the organism name. Anyways, you can use [bedtools getfasta][1] to extract regions from a fasta file using coordinates specified in bed/gff format. [1]: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.h ...
written 4 weeks ago by ashish320
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Answer: A: GO annotation with entrez gene id for non-model organism
... Usually one would BLAST the sequences and then use those results to retrieve GO terms. BLAST2GO uses this approach but the BLAST part of it is very slow and I am not sure if there is a way to access BLAST2GO using R. You can create your own annotation package for any organism using the [AnnotationFo ...
written 5 weeks ago by ashish320
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Comment: C: Low Complexity region determination using SEG
... Thanks for clarifying. Recent blast versions do not give a summary like that as far as i know. ...
written 5 weeks ago by ashish320
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Comment: C: Low Complexity region determination using SEG
... I think seg now comes with the ncbi blast package. ...
written 5 weeks ago by ashish320
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Comment: C: Parameters for variant calling in genome of unknown ploidy
... This may help https://edepot.wur.nl/441939 ...
written 7 weeks ago by ashish320
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Answer: A: RNA seq with 2 biological replicates
... I hope you know the importance of replicates in transcriptome studies. Having said that you need to search for transcriptome studies on plants where sample collection is difficult. You should search the web for such plants. Don't expect people to do the search for you. Litchi is one such plant. Flo ...
written 8 weeks ago by ashish320
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Comment: C: How to find a pathway from genes to disease
... Is it a plant or an animal? For mouse, you can try [MGI][1]. It has information on genes-disease connection as well. For pathway, you can also try [Reactome][2]. Both are very user-friendly. Reactome has version of [plants][3] as well. [1]: http://www.informatics.jax.org/ [2]: https://reactome ...
written 9 weeks ago by ashish320

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Popular Question 5 days ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 10 days ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Great Question 22 days ago, created a question with more than 5,000 views. For retrieving best hit in local blast output
Great Question 3 months ago, created a question with more than 5,000 views. For heatmap using FPKM values
Great Question 4 months ago, created a question with more than 5,000 views. For levels in gene ontology
Centurion 4 months ago, created 100 posts.
Voter 6 months ago, voted more than 100 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 14 months ago, created a question with more than 1,000 views. For Gap treatment in MEGA for ML phylogeny
Popular Question 14 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 14 months ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 18 months ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 18 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 18 months ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 19 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 21 months ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 23 months ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 2.1 years ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
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Scholar 3.2 years ago, created an answer that has been accepted. For A: please help me retrieve these sequences

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