User: swadha

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swadha20
Reputation:
20
Status:
New User
Location:
University of California, United States
Last seen:
3 months, 3 weeks ago
Joined:
5 years, 7 months ago
Email:
s*******@gmail.com

PhD Student

Posts by swadha

<prev • 22 results • page 1 of 3 • next >
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Comment: C: To fetch the reads which are being partially mapped to the genome
... 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 4 months ago by swadha20
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Comment: C: To fetch the reads which are being partially mapped to the genome
... 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 ...
written 4 months ago by swadha20 • updated 4 months ago by genomax62k
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To fetch the reads which are being partially mapped to the genome
... 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 ...
jvarkit hisat2 star rna-seq bowtie2 written 4 months ago by swadha20 • updated 4 months ago by genomax62k
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Comment: C: Is it possible to visualize ChIP peaks of three different samples in one plot us
... It is working now! Thank you! ...
written 4 months ago by swadha20
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Comment: C: Is it possible to visualize ChIP peaks of three different samples in one plot us
... 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 4 months ago by swadha20
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Comment: C: Is it possible to visualize ChIP peaks of three different samples in one plot us
... Thanks for getting back. I will definitely look into HOMER's kit ...
written 4 months ago by swadha20
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Is it possible to visualize ChIP peaks of three different samples in one plot using ChIPseeker?
... 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 ...
bdg chip-seq chipseeker written 4 months ago by swadha20 • updated 4 months ago by ZZzzzzhong190
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Comment: C: Extraction of partially mapped reads from BAM
... 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 5 months ago by swadha20
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Comment: C: Extraction of partially mapped reads from BAM
... 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 5 months ago by swadha20
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Annotating chromatin interactions (interactions generated from HOMER)
... 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 ...
hi-c homer written 22 months ago by swadha20

Latest awards to swadha

Popular Question 20 months ago, created a question with more than 1,000 views. For Peak annotation using ChIPseeker (bioconductor package)
Popular Question 20 months 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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