User: s.singh
s.singh • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- University of California, United States
- Last seen:
- 4 months, 3 weeks ago
- Joined:
- 6 years, 11 months ago
- Email:
- s*******@gmail.com
PhD Student
Posts by s.singh
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Comment:
C: How does samtools markdup works?
... Thanks a lot for the clarification. This helps a lot! ...
written 4 months ago by
s.singh • 20
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... Hi,
I am using **samtools markdup -r** parameter to remove PCR duplicates from my mapped ChIP reads. How does it detects the PCR duplicated reads?
Please let me know if I am understanding it correctly. This is what I understood:
I need to name sort the mapped reads and put MS-MC tags (using fixma ...
written 4 months ago by
s.singh • 20
• updated
4 months ago by
chaudharyc61 • 20
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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 19 months ago by
s.singh • 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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5 follow
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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 19 months ago by
s.singh • 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 20 months ago by
s.singh • 20
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... Thanks for getting back. I will definitely look into HOMER's kit ...
written 20 months ago by
s.singh • 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 20 months ago by
s.singh • 20
• updated
20 months ago by
ZZzzzzhong • 210
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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 20 months ago by
s.singh • 20
Latest awards to s.singh
Popular Question
19 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)
Popular Question
19 months ago,
created a question with more than 1,000 views.
For ChIP data analysis high binding sites
Popular Question
3.0 years ago,
created a question with more than 1,000 views.
For Peak annotation using ChIPseeker (bioconductor package)
Popular Question
3.0 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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