User: zhuobaowen

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zhuobaowen10
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Posts by zhuobaowen

<prev • 14 results • page 1 of 2 • next >
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Answer: A: TSS metaprofile using Deeptools
... You can just download a GTF file from Ensembl or UCSC and use that. computeMatrix will figure out where the TSS and TES for each transcript is then. ADD COMMENT • linkwritten 3.3 years ago by Devon Ryan ♦ 96k ...
written 6 weeks ago by zhuobaowen10
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Comment: C: How Are Paired-End Read Insert Sizes Inferred For Reporting In A Sam File?
... Thank you so much, I've been looking for this answer for a long time. ...
written 8 weeks ago by zhuobaowen10
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Comment: C: nags.plot.r outputs flat graphs and no results
... Maybe you can try Deeptools to profile the heatmap ...
written 8 weeks ago by zhuobaowen10
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Comment: C: How to handle 4 fastq file for one paired-end sample?
... sorry, I just use cat command to add the fastq data, or use samtools merge to merge bam data ...
written 9 weeks ago by zhuobaowen10
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Comment: C: How to handle 4 fastq file for one paired-end sample?
... IN1_S1_L001_R1_001.fastq, L001 and L002 means different lanes, R1 and R2 means read1 and matched read2. so you should use R1F=IN1_S1_L001_R1_001.fastq, R1R=IN1_S1_L001_R2_001.fastq as input 1 and 2, or merge the different lane data into a one data, then use bowtie2. ...
written 9 weeks ago by zhuobaowen10
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Comment: C: How to get nucleotide sequence of the foxp3 enhancer ?
... OK,thank you so much ...
written 9 weeks ago by zhuobaowen10
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Comment: C: How to get nucleotide sequence of the foxp3 enhancer ?
... yes, I only get the sequence of transcrips of FOXP3 from NCBI GENE database, but I don't know the location of CNS. ...
written 9 weeks ago by zhuobaowen10
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How to get nucleotide sequence of the foxp3 enhancer ?
... Hello everyone, I am doing some research on the regulation of FOXP3 expression, FOXP3 has three enhancers, also known as CNS1, CNS2, CNS3, but I want to get the nucleotide sequence of the FOXP3 enhancer and its location. Does anyone know how to search it and get it? Thank you so much! ...
chip-seq rna-seq written 9 weeks ago by zhuobaowen10 • updated 9 weeks ago by Alex Nesmelov110
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Comment: C: ATAC-seq sample normalization (quantil normalization)
... you are right, thank you so much! ...
written 5 months ago by zhuobaowen10
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Comment: C: ATAC-seq sample normalization (quantil normalization)
... Hello, I have got the scale factor according to your method, but I'm not sure which is right. can you help me to judge which is right? thank you! here is my code bamCoverage --bam sample147.final.bam -o sample147.TMM.bw --binSize 50 --scaleFactor 0.04000290 --numberOfProcessors 4 bamCovera ...
written 5 months ago by zhuobaowen10

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