User: Chirag Parsania
Chirag Parsania • 240
- Reputation:
- 240
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- Location:
- University of Macau
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- Google Scholar Page
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- Joined:
- 1 year, 11 months ago
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- c**************@gmail.com
Posts by Chirag Parsania
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... 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 Parsania • 240
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... 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 Parsania • 240
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... One of the solution I found here
https://support.bioconductor.org/p/72656/
...
written 6 days ago by
Chirag Parsania • 240
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... 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_ ...
written 6 days ago by
Chirag Parsania • 240
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... 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 Parsania • 240
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... 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 ...
written 8 days ago by
Chirag Parsania • 240
• updated
8 days ago by
kristoffer.vittingseerup • 80
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... 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 Parsania • 240
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... 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 Parsania • 240
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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 Parsania • 240
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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 Parsania • 240
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22 days ago,
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For Extract reads from bam/sam files using read id
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6 months ago,
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For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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created an answer with at least 3 up-votes.
For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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