User: lin.pei26

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lin.pei2660
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New User
Location:
China
Last seen:
6 months, 3 weeks ago
Joined:
3 years, 11 months ago
Email:
l********@gmail.com

Posts by lin.pei26

<prev • 49 results • page 1 of 5 • next >
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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 2.3 years ago by lin.pei2660 • updated 2.1 years ago by Suzanne50
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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 2.3 years ago by lin.pei2660
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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 2.3 years ago by lin.pei2660 • updated 2.3 years ago by genomax58k
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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 2.3 years ago by lin.pei2660
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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 2.5 years ago by lin.pei2660
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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 2.5 years ago by lin.pei2660
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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 2.5 years ago by lin.pei2660
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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 2.5 years ago by lin.pei2660
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a protein failed to be aligned to genome by tblastn
... Hi all: I have a protein sequence which I know the genomic region where it came from. also I have the CDS. by blasting the CDS to the genome, I can find the exact position of that transcript. however, the first 200 AA of the protein could not be aligned to the corresponding region by **tblastn**. ...
blast written 2.5 years ago by lin.pei2660
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Comment: C: align two long sequences using Muscle but found gaps only
... Thanks for the reply! ...
written 2.7 years ago by lin.pei2660

Latest awards to lin.pei26

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