User: Ambika

gravatar for Ambika
Ambika30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
2 months, 3 weeks ago
Joined:
2 years, 11 months ago
Email:
a***************@gmail.com

Posts by Ambika

<prev • 106 results • page 1 of 11 • next >
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Comment: C: Gene prediction programs predicting different genes
... Alex, thanks for the suggestion. will surely try this. ...
written 11 weeks ago by Ambika30
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Comment: C: Gene prediction programs predicting different genes
... Juke, I have a bam file generated from STAR alignment. I will use this file to see if its merged or not. Thanks!! ...
written 11 weeks ago by Ambika30
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Comment: C: Gene prediction programs predicting different genes
... JC, I have not done RT-PCR on my knocked strain, howeverr this is something I can do sooner. Thanks for the suggestion!!! ...
written 11 weeks ago by Ambika30
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Comment: C: Gene prediction programs predicting different genes
... Genomax, what about the fact that the 178 bp region does not have promoter sequence? Can we still consider the second part as a separate gene? ...
written 12 weeks ago by Ambika30
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Comment: C: Gene prediction programs predicting different genes
... Genomax, I will look into this RACE assay, if it would help me distinguish the genes it would be great. Thanks ...
written 12 weeks ago by Ambika30
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Comment: C: Gene prediction programs predicting different genes
... Alex, blasted my gene in NCBI and found that in the closely related species and the size of the gene is around 1.6 Kb too. Interesting thing is that both genes predicted from funnotate have same PFAM domain. Because of this I thought may be there is gene duplication but they are not similar. ...
written 12 weeks ago by Ambika30
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Comment: C: Gene prediction programs predicting different genes
... JC, I did RT-qPCR before to validate the gene expression and I designed my primers around the 3' end so it has the amplicon only from second gene. So, now to confirm do you think I need to design primer that could amplify the region from both genes? Thanks for the suggestion, I will look for the sp ...
written 12 weeks ago by Ambika30
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Gene prediction programs predicting different genes
... Hello everyone, In this past couple of weeks I encountered a different problem which is giving me a lot of stress, I hope you can give me some suggestions. I did RNAseq analysis in a fungal species year ago using a genome file and genes predicted from AUGUSTUS ( which were generated by my lab membe ...
genome annotation augustus rnaseq funannotate written 12 weeks ago by Ambika30 • updated 12 weeks ago by Juke344.5k
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Comment: C: MUMmer alignment result interpretation
... It is not a complete table I have some overlap regions more than 20kb as well. I do have the gene annotation file. Do you think comparing the protein sequences will help in distinguishing the accessory region of the genome. And thank you for suggesting that program I will look into that. ...
written 4 months ago by Ambika30
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MUMmer alignment result interpretation
... Hello Biostars, I am doing whole genome alignment using NUCmer (a program under MUMmer). I am using this alignment to separate core and accessory chromosome. From NUCmer alignment I generated delta files which I filtered using options -r and -g and generated the coordinate file. This coordinate fil ...
genome mummer alignment nucmer written 4 months ago by Ambika30

Latest awards to Ambika

Centurion 12 weeks ago, created 100 posts.
Popular Question 3 months ago, created a question with more than 1,000 views. For Cuffmerge error while merging gtf files
Great Question 4 months ago, created a question with more than 5,000 views. For Feature Counts output interpretation
Great Question 9 months ago, created a question with more than 5,000 views. For Unable to access jarfile trimmomatic-0.35
Popular Question 9 months ago, created a question with more than 1,000 views. For Interpretation of Results from trimmomatic
Popular Question 9 months ago, created a question with more than 1,000 views. For HTseq Pysam error
Popular Question 9 months ago, created a question with more than 1,000 views. For stranded vs not stranded Htseq-output differences
Popular Question 9 months ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Popular Question 12 months ago, created a question with more than 1,000 views. For Cufflinks gtf file to htseq
Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2 workflow for RNAseq
Supporter 13 months ago, voted at least 25 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Deseq2 library load error
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Unable to access jarfile trimmomatic-0.35
Popular Question 2.1 years ago, created a question with more than 1,000 views. For HTseq Pysam error
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Trimmomatic jar file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Interpretation of Results from trimmomatic
Popular Question 2.1 years ago, created a question with more than 1,000 views. For HTseq error: Too few arguements
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq2 workflow for RNAseq
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Feature Counts output interpretation
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Unable to access jarfile trimmomatic-0.35
Rising Star 2.7 years ago, created 50 posts within first three months of joining.

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