User: s.singh
s.singh • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- University of California, United States
- Last seen:
- 1 month, 1 week ago
- Joined:
- 7 years, 8 months ago
- Email:
- s*******@gmail.com
Grad Student
Posts by s.singh
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2
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... Hi Everyone,
For *C.elegans*, the HTseq output files have 46,779 genes (WB gene names). Worms should only have ~20,000 coding genes. Does anyone know why we have 2x more genes in our output? Does this include non-coding genes?
Thanks
S ...
written 9 weeks ago by
s.singh • 20
• updated
9 weeks ago by
WouterDeCoster ♦ 45k
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... Hey,
Thanks so much for pointing to this. I somehow had missed this.
I didn't know that there was such thing as "Table Browser" available on UCSC.
Thanks a lot!
-S ...
written 7 months ago by
s.singh • 20
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... Hi,
I am trying to do a raw read count (FPKM) for my RNAseq data using RseQC. The data I have is of *C.elegans* and I am not sure where to find its "Reference gene model bed file". RseQC is not accepting GTF/GFF file.
Can you suggest other tools which can find FPKM for my RNAseq data?
Thanks
-S ...
written 7 months ago by
s.singh • 20
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... Technical replicates in my case are replicates where the biological material is the same but they are sequenced at different times.
The organism is *C. elegans*. I know the mapping scores are very low. I just feel like it is hard to get a good ChIP all together. ...
written 8 months ago by
s.singh • 20
0
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... Hi,
I have two biological replicates of histone ChIP. Each biological replicates has its own technical replicate. I mapped the ChIP reads using bowtie-1 (because I wanted to use -m 2 parameter and it was single end 50 BP long reads). I then removed the PCR duplicates from each of the datasets usin ...
written 8 months ago by
s.singh • 20
0
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2
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Comment:
C: How does samtools markdup works?
... Thanks a lot for the clarification. This helps a lot! ...
written 13 months ago by
s.singh • 20
8
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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 13 months ago by
s.singh • 20
• updated
13 months ago by
chaudharyc61 • 40
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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 2.4 years ago by
s.singh • 20
0
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585
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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 ...
1
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585
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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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7 weeks ago,
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For Annotating chromatin interactions (interactions generated from HOMER)
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For ChIP data analysis high binding sites
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For Peak annotation using ChIPseeker (bioconductor package)
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For cant find full annotated genomes of two strains of mouse (C57BL/6NJ and BALB/cJ)
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