User: s.singh

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s.singh20
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

<prev • 29 results • page 1 of 3 • next >
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Does HTSEQ output include non-coding genes also?
... 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 ...
htseq rnaseq ngs c.elegans worms written 9 weeks ago by s.singh20 • updated 9 weeks ago by WouterDeCoster45k
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Comment: C: Where to find reference gene model for C. elegans to compute FPKM using RseQC?
... 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.singh20
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Where to find reference gene model for C. elegans to compute FPKM using RseQC?
... 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 ...
rnaseq next-gen rseqc written 7 months ago by s.singh20
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Comment: C: ChIP-seq technical replicates giving very different percentage mapping score. Is
... 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.singh20
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ChIP-seq technical replicates giving very different percentage mapping score. Is it normal?
... 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 ...
chipseq chip next-gen bowtie sequencing written 8 months ago by s.singh20
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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.singh20
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How does samtools markdup works?
... 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 ...
samtools markdup written 13 months ago by s.singh20 • updated 13 months ago by chaudharyc6140
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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 2.4 years ago by s.singh20
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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 2.4 years ago by s.singh20 • updated 2.4 years ago by GenoMax96k
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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 2.4 years ago by s.singh20 • updated 2.4 years ago by GenoMax96k

Latest awards to s.singh

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Annotating chromatin interactions (interactions generated from HOMER)
Popular Question 7 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 13 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 13 months ago, created a question with more than 1,000 views. For ChIP data analysis high binding sites
Popular Question 2.3 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)
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ChIP data analysis high binding sites
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Peak annotation using ChIPseeker (bioconductor package)
Popular Question 3.7 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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