User: Chirag Parsania

gravatar for Chirag Parsania
Reputation:
240
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Location:
University of Macau
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1 day, 16 hours ago
Joined:
1 year, 11 months ago
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Posts by Chirag Parsania

<prev • 54 results • page 1 of 6 • next >
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Comment: C: How to improve existing transcriptome annotation using cufflink protocol ?
... yes... I know these options. My data is strand specific (`--rf`) so I used string tie accordingly. I also tried another option (`--fr`) to confirm if my library option is correct. Still there is an issue. EDIT : More precisely most of them are in correct orientation. But still there are cases whic ...
written 2 days ago by Chirag Parsania240
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Comment: C: How to improve existing transcriptome annotation using cufflink protocol ?
... Hi Vijay, I have used stringtie. Results are more or less same with cufllink. I decided not to merge transcripts from different samples rather use individual assembly and filter them manually by user specified criteria. Merging assembly in fugal genome may not good idea because genes are very close ...
written 2 days ago by Chirag Parsania240
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Comment: C: How to find more than 'n %' overlapping ranges using GRanges package ?
... One of the solution I found here https://support.bioconductor.org/p/72656/ ...
written 6 days ago by Chirag Parsania240
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How to find more than 'n %' overlapping ranges using GRanges package ?
... Hi, I have two dataframes (in R) A and B of Granges. feature mentioned in the B is within the feature of A. > a GRanges object with 2 ranges and 0 metadata columns: seqnames ranges strand [1] ChrD_C_glabrata_ ...
R genomicranges granges written 6 days ago by Chirag Parsania240
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Comment: C: How to improve existing transcriptome annotation using cufflink protocol ?
... Hi Vijay, Good to know this new transcriptome assembler (though published in 2014). Seems actively updated vs cufflink (last release 2014). I will try this and share the results. Thanks a lot. ...
written 8 days ago by Chirag Parsania240
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How to improve existing transcriptome annotation using cufflink protocol ?
... I am working on fungi transcriptome. Existing annotation for my species is not reliable. To improve the annotation we generated RNAseq data with different stress conditions to make all transcripts to express in different conditions and using those expressed transcripts in different conditions I am t ...
assembly cufflink cuffmerge transcriptome written 8 days ago by Chirag Parsania240 • updated 8 days ago by kristoffer.vittingseerup80
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Answer: A: simoultaneous chromatin + transcriptional profiling
... HI, I would suggest you to explore recent papers of chip and RNAseq. Definitely you will find some with both chip and RNAseq. You haven't mentioned which organism you are looking for. Here is the one from our lab for yeast *candida albicans* contains TF chip, H3 chip, polII chipseq and RNAseq. All ...
written 24 days ago by Chirag Parsania240
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Answer: A: Gene set enrichment analysis tools
... Hi, There are so many GSEA tools. GSEA is one of them. Other than I like following two 1) [topGO][1] 2)[Bingo][2] [1]: http://bioconductor.org/packages/release/bioc/html/topGO.html [2]: https://www.psb.ugent.be/cbd/papers/BiNGO/Home.html ...
written 24 days ago by Chirag Parsania240
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Comment: A: NR BLAST on AWS
... I am using sbatch command to submit job on hpc through sh script. see the script below #!/bin/bash #SBATCH --job-name NR_BLAST #SBATCH --partition FHS_LONG #SBATCH --nodes 1 #SBATCH --tasks-per-node 24 #SBATCH --mem 128g #SBATCH --time 124:00:00 #SBATCH ...
written 4 weeks ago by Chirag Parsania240
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Comment: C: NR BLAST on AWS
... Hi Jacob, Thanks for useful suggestion. Blast has already been install on amazone by NCBI. you can check it [here][1]. They also provide perl script to run blast on AWS server. I am not sure about database. User may need to download the blast database in his/her amazone instance or it has also been ...
written 4 weeks ago by Chirag Parsania240

Latest awards to Chirag Parsania

Popular Question 22 days ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 10 months ago, created a question with more than 1,000 views. For Z-Score calculation by heatmap.2

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