User: Alexie Li

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Alexie Li20
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4 months, 3 weeks ago
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Posts by Alexie Li

<prev • 10 results • page 1 of 1 • next >
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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 9 weeks 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 months 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 months ago by Alexie Li20 • updated 3 months 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 4 months 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 4 months 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 4 months 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 4 months ago by Alexie Li20 • updated 4 months ago by Pierre Lindenbaum102k
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Comment: C: how to write a script to grep the lowest e-value for each gene?
... Actually, they are a merged file of results generated by different methods, I want to check which method generally give the best results or more reliable. ...
written 4 months ago by Alexie Li20
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how to write a script to grep the lowest e-value for each gene?
... Hi all, I have a file containing blast hits for each gene, one hit per line, as following ID E-value g1 0.0 g1 1e-20 g1 1e-5 g2 1e-5 g2 1e-13 g3 0.01 I would like to grep the lowest e-value for each gene, how to write a script to make it? ...
script linux written 4 months ago by Alexie Li20 • updated 4 months ago by venu4.5k
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how to write scripts to split GO terms as one per line
... Hi all, I got a file with the first column containing id and second column containing annotated gene ontology numbers. As the following CPIW_00004002-RA GO:0005515 CPIW_00004002-RA GO:0010997|GO:0097027|GO:1904668 CPIW_00004003-RA GO:0003824|GO:0008152 CPIW_00004003-RA GO:0003987|GO:0016208|GO ...
perl python file format linux written 4 months ago by Alexie Li20 • updated 4 months ago by Chirag Parsania430

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