User: Alexie Li

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Alexie Li20
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20
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New User
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2 years, 5 months ago
Joined:
3 years, 7 months ago
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y********@gmail.com

Posts by Alexie Li

<prev • 13 results • page 1 of 2 • next >
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WGCNA module interpretation question
... I am using WGCNA to generate gene co-expression network. I am confused about the how to interpret gene module colors. My understanding is, different modules will have different color. So the downstream analysis could be based a specific colored module such as blue. However, the cluster dendrogram fi ...
wgcna co-expression network written 2.6 years ago by Alexie Li20 • updated 2.6 years ago by EagleEye6.8k
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Anyone knows how to create a figure like this?
... Horizontal axis indicate features on chromosomes. Y axis displays multiple chromosomes. Thank you! Best wishes, Alexie Li ...
genome visualizaion tool written 2.9 years ago by Alexie Li20 • updated 2.9 years ago by Ram32k
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genomes with lower identity display closer relationship than genomes with higher identity, any idea why?
... Hi all, I have alignment five close-related genomes. A, B, C, D and E. A and B share nucleotide level identity as 96%, while between A and C this number is 94%. I used several methods to build their phylogeny trees. All the result showed A is closer to C and B. I am curious why. Shouldn't the genom ...
phylogeny evolution identity written 3.1 years ago by Alexie Li20
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Are regular illumina poly(a) rna-seq data suitable to study polyadenylation sites?
... Hi all! I have a question about is there a particular requirement for RNA-seq to study poly(A) in a species? I have many rna-seq data using poly(A) based library preparation method, but they are not designed to study alternative polyadenylation problem. From my understanding, the data should harbor ...
poly(a) sites rna-seq written 3.4 years ago by Alexie Li20
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Comment: C: how to explain expression level peaks(uneven gene expression) within a gene?
... I think maybe I understand what is happening with the uneven expression. FastQC showed enriched clusters at the beginning of reads which means the library is biased by random priming during library preparation. Maybe it is why... ...
written 3.5 years ago by Alexie Li20
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Are all antisense transcripts from polyA enriched library RNA-seq polyadenylated?
... Dear all, I have a confusion about antisense detection. From my RNA-seq result which is strand-specific and polyA enriched during library preparation, about one-third of genes showed antisense expression. Does it mean all the antisenses detected here have polyA tails/polyadenylated? Thank you for y ...
antisense polyadenylation rna-seq written 3.5 years ago by Alexie Li20 • updated 3.5 years ago by chalchiuhticuenaabah0
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how to explain expression level peaks(uneven gene expression) within a gene?
... Hi all, I have a question about gene expression. I mapped RNA-seq reads back to the genome and noticed there are my expression peaks within a gene. Does it cause by library preparation process, sequencing problem, or a real biological thing? The blue bar on the top is a gene(single-exon gene), the r ...
assembly expression rna-seq written 3.6 years ago by Alexie Li20
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Comment: C: how to write a script to grep information from another file without losing locat
... It worked! Thank you. ...
written 3.6 years ago by Alexie Li20
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Comment: C: how to write a script to grep information from another file without losing locat
... Hi russhh! Thank you for your help. I tried this method but failed to get the result, I think there are two problems 1)I can't sort file 1 since I need the order information 2)For some reason, my system is not recognizing "join -t $'\t'" and gave the error message "join: illegal tab character spec ...
written 3.6 years ago by Alexie Li20
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how to write a script to grep information from another file without losing location information(in the right order)
... Hi all I am too new with programing to solve this problem. I have two files, file1 containing the index, file2 includes information I want. 1. file1 CU_91 CU_495 CW_79 CU_22 CW_42 2. file2 CW_79 protein1 CW_15 protein ...
script linux written 3.6 years ago by Alexie Li20 • updated 3.6 years ago by Pierre Lindenbaum134k

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