User: ancient_learner

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I am a Bioinformatician dealing with NGS data analysis

Posts by ancient_learner

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Comment: C: Analysis pipeline for 3e Hi-C
... Could be. But What would be the advantage of such approach? ...
written 9 months ago by ancient_learner610
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Analysis pipeline for 3e Hi-C
... Hi I recently came across with [this paper][1] in which Chromatin was subsequently digested with three enzymes. According to my knowledge the restriction site is pretty much used in QC to obtain valid Hi-C pairs. But since, they have used 3 enzymes I am unable to find how they filtered the sequenc ...
hi-c 3e hi-c multi-enzyme digestion written 9 months ago by ancient_learner610
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Comment: C: Iterative trimming using bowtie
... Yeah. [GSE74912][1] [1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74912 ...
written 9 months ago by ancient_learner610
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Comment: C: Iterative trimming using bowtie
... Yes. Thought I would grep them out after alignment. ...
written 9 months ago by ancient_learner610
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Comment: C: Iterative trimming using bowtie
... The reason I chose to do iterative mapping is after adapter trimming only 56% of the reads are getting Uniquely aligned to the reference genome. Where as around 10-15% are getting aligned to multiple locations. I thought If I could somehow retain those as well that would add up to my alignment perce ...
written 9 months ago by ancient_learner610
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Iterative trimming using bowtie
... Hi I want to use bowtie2 and align the sequenced reads(length=76) to hg38. I have trimmed to get 30 bp long reads and performed alignment. Reads that mapped to multiple regions in the genome were to be extended by 5 bp and then re-mapped. This process will be repeated until either all reads were un ...
bowtie2 iterative trimming alignment atac-seq written 9 months ago by ancient_learner610 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: Nextera Transposon Contamination
... here is the link [Illumina Adapter Sequences ][1] [1]: https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences-1000000002694-09.pdf ...
written 10 months ago by ancient_learner610
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Comment: C: ATAC-seq DE analysis
... **Just a quick question:** Would it be possible to identify allele specific chromatin accessibility regions (ATAC-Seq) through snakePipes ...
written 10 months ago by ancient_learner610
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Identifying ago2 enriched genes under 2 different conditions
... We wanted to see the effect of particular gene expression (gene A) over mirna targetome. for that we have designed our experimental setup as follows total cell RNA lysate(TL) RIP Results Condition1 ( geneA-/- cells) condition1 Ago2 enriched genes in cond1 ...
deseq2 rip-seq rna-seq written 18 months ago by ancient_learner610
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problem in bedtools pairtobed
... Hi There seems to be a problem with bedtools pairtobed command. I have used the following command to check whether both ends in my bedpe file overlap with bed file. my bedpe file contains 6 columns (chr,start1,end1, chr,start2,end2).However I am surprised to see the output pairToBed -a bedpe_f ...
bedtools written 3.3 years ago by ancient_learner610

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