User: lin.pei26

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lin.pei2640
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New User
Location:
China
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4 months, 4 weeks ago
Joined:
2 years, 11 months ago
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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 16 months ago by lin.pei2640 • updated 13 months 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 16 months ago by lin.pei2640
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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 16 months ago by lin.pei2640 • updated 16 months ago by genomax37k
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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 16 months ago by lin.pei2640
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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 18 months ago by lin.pei2640
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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 18 months ago by lin.pei2640
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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 18 months ago by lin.pei2640
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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 18 months ago by lin.pei2640
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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 18 months ago by lin.pei2640
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Comment: C: align two long sequences using Muscle but found gaps only
... Thanks for the reply! ...
written 20 months ago by lin.pei2640

Latest awards to lin.pei26

Popular Question 16 months ago, created a question with more than 1,000 views. For what is the difference between reference genome sequence from UCSC and ensembl ?
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Scholar 18 months ago, created an answer that has been accepted. For A: a protein failed to be aligned to genome by tblastn
Popular Question 21 months ago, created a question with more than 1,000 views. For what should be the expected result of cuffmerge?
Popular Question 22 months ago, created a question with more than 1,000 views. For tophat, the parameter "Expected inner distance between mate pairs"?

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