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User: xiaoguang

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xiaoguang • 50
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Posts by xiaoguang

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Differential analysis isoform level or gene level ?
... I think some other methods like genome aligned based can get the accurate expression count of gene-level. such as subread+featureCount? ...
written 6 weeks ago by xiaoguang • 50
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Comment: C: how to get the geneNames or bedfile from fasta sequences
... also ,excel can help you ...
written 6 weeks ago by xiaoguang • 50
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Comment: C: how to get the geneNames or bedfile from fasta sequences
... probably you need python or R？Maybe you should parse your coordinate to chromosome, start,end,strand. then make a six column file delimited by "\t", which contains chromosome,start,end,name,score and strand. ...
written 6 weeks ago by xiaoguang • 50
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Comment: C: how to get the geneNames or bedfile from fasta sequences
... I think you must have one complete reference genome, otherwise you can not get the filtered fasta file. you first download local ncbi-blast program and using your reference to make database. Then you can blast your motif to your reference database to get coordinates ...
written 6 weeks ago by xiaoguang • 50
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Comment: C: Filtering BAM files efficiently
... the iteration of python is to much slow, so I think you can use some other language like perl or bash, to warp samtools to do that ...
written 6 weeks ago by xiaoguang • 50
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Comment: C: Differential analysis isoform level or gene level ?
... yes, if you use tximport, it actually sum all isoform counts from their gene as gene-level count. ...
written 6 weeks ago by xiaoguang • 50
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Answer: A: How to count the number of alignments in a bam file without using samtools?
... Bam file is a binary file stroing alignment information, so we must need htslib.h api to interprete that. if you use GNU, you need htslib.h. if you use python, pysam must be the best choice for you. ...
written 6 weeks ago by xiaoguang • 50
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Answer: A: how to get the geneNames or bedfile from fasta sequences
... you can use ncbi-blast to realign this motif sequence to your reference. ...
written 6 weeks ago by xiaoguang • 50
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Can I use the SCENIC package to analyze the transcription factors in the bulk RNAseq data?
... The SCENIC package is software for the analysis of transcription factor activity and localized genes in single-cell transcriptome sequencing data, and the R package also scores the transcription factor activity of each cell. can I use the pack for bulk seq? ...
scenic rna-seq written 9 months ago by xiaoguang • 50 • updated 9 months ago by geek_y ♦ 11k
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Comment: C: Open Source Mass Spec Search Engines?
... Is there any tutorial for X! Tandem software, I have n’t found it for a long time ...
written 9 months ago by xiaoguang • 50

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For proj_api.h not found in standard or given locations
Popular Question 6 months ago, created a question with more than 1,000 views. For proj_api.h not found in standard or given locations
Popular Question 6 months ago, created a question with more than 1,000 views. For How to normalized TPM with TMM method?
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