User: lin.pei26

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lin.pei2690
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Posts by lin.pei26

<prev • 51 results • page 1 of 6 • next >
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Comment: C: What tool can be used to predct regulatory element within an input sequence ?
... Thank you jrj.healey ! I will have a check! ...
written 4 months ago by lin.pei2690
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What tool can be used to predct regulatory element within an input sequence ?
... Hi all: is there any tools that can be used to scan an input sequence and predict any potential regulatory element within that sequence? in fact i got one such sequence (chicken) which was supposed to be bound by some regulator, e.g., TF, however, we are not sure what the exact regulator is? so I ...
sequence written 5 months ago by lin.pei2690 • updated 4 months ago by Gautier Richard280
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how to improve multiple sequence alignment by removing outlier sequence ?
... Hi all: Have you tried to remove outlier sequence after constructing a multiple sequence alignment ? Is there any recommended tools for this aim ? Thanks in advance! Best, ...
alignment written 3.0 years ago by lin.pei2690 • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: tophat: the Searching for junctions via segment mapping was skipped.
... not empty. That file had 141909 lines, and the step "Searching for junctions via segment mapping" takes about 5 minutes However, in another dataset SRR1915443, this junctions.bed had 143339 lines, and the step "Searching for junctions via segment mapping" takes more than 1 hours. both were using mm ...
written 3.0 years ago by lin.pei2690
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Comment: A: tophat: the Searching for junctions via segment mapping was skipped.
... Thank you. my cmd was: tophat2 -G Mus_musculus.GRCm38.83.gtf -p 4 -o tophat_out --transcriptome-index=mm10transcriptome/known mm10dna **SRR306769**.fastq the data I used was downloaded from NCBI: GSE30352 ...
written 3.0 years ago by lin.pei2690 • updated 3.0 years ago by genomax69k
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tophat: the Searching for junctions via segment mapping was skipped.
... Hi all: in tophat work, there was a step: Searching for junctions via segment mapping, which was run by **segment_juncs** however, when dealing with some mouse data, I found that this step was finished in about 2 minutes, which would be longer when processing other data. it seemed that this step w ...
rna-seq written 3.0 years ago by lin.pei2690
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align RNA-seq reads to annotated CDS
... Hi all: when performed a RNA-seq data processing, we usually align reads to the genome. I just have a simple questions: for species with a good annotation, like human, could one just align RNA-seq reads directly to the annotated CDS to quantify/estimate the abundance of known transcripts ? what is ...
rna-seq written 3.2 years ago by lin.pei2690
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Comment: C: a protein failed to be aligned to genome by tblastn
... Thanks. I modify my comment, making it clear enough to follow my original question. ...
written 3.2 years ago by lin.pei2690
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Answer: A: a protein failed to be aligned to genome by tblastn
... I solved this problem by turing off two options of tblastn: -seg and -comp_based_stats. the former was for filtering low-complexity sequence. [1] http://community.gep.wustl.edu/repository/course_materials_WU/annotation/Annotation_Strategy_Guide.pdf ...
written 3.2 years ago by lin.pei2690
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Comment: A: a protein failed to be aligned to genome by tblastn
... Thanks! I have tried this but found that the first 200 AA could not be aligned to genome by tblastn when using this 200AA as query alone. as a control, another 200AA in the middle of the protein could be aligned to the correct position with a %identity < 60%. ...
written 3.2 years ago by lin.pei2690

Latest awards to lin.pei26

Popular Question 3 months ago, created a question with more than 1,000 views. For low mapping rate when using SRA RNA-seq data
Great Question 14 months ago, created a question with more than 5,000 views. For tophat, the parameter "Expected inner distance between mate pairs"?
Popular Question 14 months ago, created a question with more than 1,000 views. For low mapping rate when using SRA RNA-seq data
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Scholar 3.2 years ago, created an answer that has been accepted. For A: a protein failed to be aligned to genome by tblastn
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