User: swadha
swadha • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- University of California, United States
- Last seen:
- 8 months, 2 weeks ago
- Joined:
- 6 years ago
- Email:
- s*******@gmail.com
PhD Student
Posts by swadha
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... I am trying to find mRNA reads which are trans-spliced (this results when protein-coding regions from multiple RNAs transcribed from different loci can be joined). I have created a fake dataset so see if Bowtie2, HISAT2 or STAR can map these type of trans-spliced reads. I can move forward with the p ...
written 9 months ago by
swadha • 20
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... I used default parameters. I was not sure which parameters can give hits for such kind of sequences. Like for Hisat I used:
hisat2 -x hisat2_ref/ref --known-splicesite-infile giardia_cis_splicesites.txt -U test_1.fq --no-sq > mapped.bam
The output I got is:
seq-1_Whole_sequence_is ...
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... Hi,
I have been trying to fetch the reads which are being partially mapped to the genome. Like if the total length of a sequence is 126 bases and only 66 bases out of 126 are mapping to the genome. Is it possible to fetch those sequences whose half of the bases align to the genome? I created a fake ...
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... It is working now! Thank you! ...
written 9 months ago by
swadha • 20
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... Thanks for getting back. Yes, I got the desired output. I am able to plot all the graphs in one plot. I have one more small question. How do I change the legends? By default, it labels the graphs as "peak1" peak2" peak3" and so forth. How do change the labels? ...
written 9 months ago by
swadha • 20
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... Thanks for getting back. I will definitely look into HOMER's kit ...
written 9 months ago by
swadha • 20
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... Hi,
I used MACS2 to call the peaks of three different ChIP samples. I have 3-bed files which I want to visualize.
I am trying to generate "**Average Profile of ChIP peaks binding to TSS region**" plot from ChIPseeker. Though I am able to generate three different "**Average Profile of ChIP peaks ...
written 9 months ago by
swadha • 20
• updated
9 months ago by
ZZzzzzhong • 200
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... I know that was a dumb question to ask but I still can't locate "samjdk.jar".
It looks like I have java installed on my server. ...
written 10 months ago by
swadha • 20
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... Hi,
Is there any other way to do it? I tried using your code but it says:
Error: Unable to access jarfile src/jvarkit-git/dist/samjdk.jar
Swadha
...
written 10 months ago by
swadha • 20
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... Hi All,
I am using HOMER to analyse Hi-C data of *Hordeum vulgare* (Barley). I have computed the significant chromatin interactions and now I want to annotate these interactions. HOMER doesn't have an inbuilt genome of barley in it, so, I am not able to annotate the interactions. I tried using GFF ...
written 2.3 years ago by
swadha • 20
Latest awards to swadha
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Peak annotation using ChIPseeker (bioconductor package)
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For cant find full annotated genomes of two strains of mouse (C57BL/6NJ and BALB/cJ)
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