User: 52Teth

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52Teth30
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2 years, 11 months ago
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3 years, 6 months ago
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Posts by 52Teth

<prev • 8 results • page 1 of 1 • next >
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Tools To Do the Alternative Splicing Analysis
... I want to do the alternative splice analysis with a set transcript sequence. The referenced genome sequence is also known.  So Is there any tools avaliable to do this? Thanks for your reply. ...
as rna-seq written 3.3 years ago by 52Teth30 • updated 3 months ago by Charles Warden6.6k
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Tools to predict genes with RNA sequence?
... I have got a set of transcript sequence from RNA-seq in fasta. The referenced genome sequence is also known. Now I want to discover new genes from the transcript sequence. So Is there any tools avaliable to do this? Thanks for your reply.   ...
gene-prediction tools rna-seq written 3.3 years ago by 52Teth30
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How can I calcualte the sequence identity and coverage form GMAP output bam file?
... Now I have got a bam file from gmap alignment with data from RNA sequencing. Now I want to get the statistic information about the coverage and identity of every sequence. So is there any tools that can deal with this?Or How can I compute the identity and coverage form sam file? Thanks a lot for any ...
gmap alignment coverage identity sam/bam written 3.3 years ago by 52Teth30 • updated 18 months ago by Biostar ♦♦ 20
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Answer: A: Tophat2 can't find Bowtie index files *.ebwt
... Thanks a lot . I have updated it and it really works.  But I am wonder what the difference between bowtie1 and bowtie2. Does it influence my result using different version of boetie? Thanks a lot again. ...
written 3.4 years ago by 52Teth30
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tophat2 aligment ratio reduced when increase insert size
... Now I have two set of HiSeq pair end equencing data for the same sample with different insert size(196 and 225). The I use tophat2 to align the reads to the genome seperately, the tophat2 parameter (--read-mismatches 2,--read-edit-dist 2,--max-intron-length 5000000,--library-type fr-unstranded,--mat ...
insert size tophat2 alignment ration rna-seq written 3.4 years ago by 52Teth30
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Comment: A: Tophat2 can't find Bowtie index files *.ebwt
... I run my job on our cluster and there is only bowtie1 is installed. So when  I run my job with tophat2, the error info is given. Now I am wonder how can I  produce index file .*.ebwt. OR has the latest tophat2 solved this issule? ...
written 3.4 years ago by 52Teth30
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Tophat2 can't find Bowtie index files *.ebwt
... I have run tophat2 using cmd: tophat2 --bowtie1 -p 6 -G /project/Ref_Genome/GRCm38.gtf -N 2 -r 40 --library-type fr-unstranded -o ./ /project/Ref_Genome/GRCm38.genome.fa /project/rawdata/mouse-1.fq /project/rawdata/mouse-2.fq but the following error occurs: Error: Could not find Bowtie index files / ...
tophat2 ebwtl bowtie1 index files ebwt written 3.4 years ago by 52Teth30
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How should I compute the sampling depth or cells when I use pacbio RNA sequencing?
... I want to do the RNA sequencing using pacbio SMRT, I have got the transcriptome information, but I don't know how many cells should I use ? And what the sampling depth is enough?Is there any method to compute? Thank for any adviceO(∩_∩)O~ ...
sampling depth smrt rna pacbio written 3.5 years ago by 52Teth30

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