User: Ar

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Ar1.0k
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aayushraman
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Posts by Ar

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Extract the overlapping paired-end reads
... Thanks! I will try it. ...
written 5 days ago by Ar1.0k
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Comment: C: Extract the overlapping paired-end reads
... Yes, I am not interested in a particular region but the regions in the entire genome where the paired-end reads R1 and R2 overlaps. ...
written 5 days ago by Ar1.0k
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Extract the overlapping paired-end reads
... Hi, I would like to know if there is a way to extract paired-end reads (and the genomic region) from the bam file where a certain part of R1 and R2 read overlaps the genomic location. For example, if R1 and R2 are the paired-end read then, I am interested in extracting this paired-end read from the ...
paired-end reads samtools written 5 days ago by Ar1.0k
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Demultiplexing inDrop dataset
... Hello Everyone, I am having issues with demultiplexing a publically available dataset on SRA (https://www.ncbi.nlm.nih.gov/sra/SRX4061030). It is a single-cell inDrop dataset and would like to know what is the best way to demultiplex it. Any advice or help would be appreciated. Thanks! ...
single-cell rna-seq in-drop dataset written 13 months ago by Ar1.0k • updated 12 months ago by Zhaorong0
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Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
... `` It is not like, the input control or IgG control for ChIP. Then do you think I should still include them for learning the model? `` You can include them but a lot of your called by ChromHMM or MACS would have false positives. Ideally, it should be a whole genome input control or IgG-treated file. ...
written 19 months ago by Ar1.0k
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Answer: A: WGCNA cannot be done to compare two conditions?
... I believe it is not the condition but the number of replicates that are required for running WGCNA. Typically, you are required to have more than 15 samples. Ideally, I would recommend more than 30 replicates for each condition. Here is the list of frequently asked questions: https://horvath.genet ...
written 19 months ago by Ar1.0k
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Answer: A: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
... Here are the answers to your questions: 1. Don't merge and run all of them together. 2. One of the first steps of ChromHMM is peak calling. Therefore, you need to use the bed files from bam files and not peak files. Although the default settings (i.e. ) would give you less stringent calls (argumen ...
written 19 months ago by Ar1.0k
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Tool: DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
... **Update**: Our manuscript has been published in Bioinformatics -- https://doi.org/10.1093/bioinformatics/btx635. **Abstract**: We propose a data-adaptive, non-parametric, and non-regression approach to remove the biological signal to prepare the data for batch detection and then apply a semi-NMF ...
scrna-seq R batcheffects tool rna-seq written 3.6 years ago by Ar1.0k
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Comment: C: ComBat (SVA) Application - Two Technical Effects
... I am sorry but for some reason the post came up on the "Biostars Latest question". I think it was because the Biostar modified your post. However, thanks for sending the paper. I will go through it. ...
written 4.3 years ago by Ar1.0k
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Comment: C: ComBat (SVA) Application - Two Technical Effects
... Here is my earlier post on Batch Correction: https://www.biostars.org/p/196430/#196528 I would recommend you to combine all the dataset you have and then get the batch information using sva function. Now sva gives you surrogate variables (which is batch plus information about other latent variables ...
written 4.3 years ago by Ar1.0k

Latest awards to Ar

Appreciated 8 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Popular Question 8 months ago, created a question with more than 1,000 views. For ENCODE 2016: Research Applications and Users Meeting
Guru 8 months ago, received more than 100 upvotes.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Appreciated 19 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Appreciated 19 months ago, created a post with more than 5 votes. For A: Limma strange low p-values.
Great Question 19 months ago, created a question with more than 5,000 views. For DESeq2 design and interaction terms
Great Question 19 months ago, created a question with more than 5,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 19 months ago, created a question with more than 1,000 views. For Public RNA-Seq and Microarray samples from same tissue
Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2 design and interaction terms
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Question 2.4 years ago, asked a question that was upvoted at least 5 times. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 2.4 years ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Popular Question 2.9 years ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Scholar 2.9 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?

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