User: yifangt86

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yifangt860
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Posts by yifangt86

<prev • 14 results • page 1 of 2 • next >
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Rcircos for Multiple tracks of Expression data
... Hello I am trying to plot expression data with Rcircos without an ideogram information. My dataframe is like this: Chr Start End Band CSR1 CSR2 CSR3 MTR1 MTR2 MTR3 chr5B 16521 20994 AeCS5B01G000100 1821.8 739.6 1234.0 1146.2 1380.0 1229.4 chr5B 60616 61023 AeCS5B01G000200 104.2 6 ...
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Answer: A: transcripts sequence preparation for RNAseq DE analysis
... Thanks genomax and h.mon! I found out the solution for my problem with [**gffread**][1], and I post it here for those who have the same problem. gffread $gff3_file -g $genome.fasta -w transcripts.fasta -w write a fasta file with spliced exons for each GFF transcript #So that th ...
written 4 weeks ago by yifangt860
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Comment: C: transcripts sequence preparation for RNAseq DE analysis
... Thanks! Kallisto manual indicates to use transcripts for index. Could you please share your idea to get transcript-level / gene-level from the indexed whole genome, if possible? Thanks again. ...
written 4 weeks ago by yifangt860
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transcripts sequence preparation for RNAseq DE analysis
... I am confused with the technical part to discriminate the transcript-level and gene-level in RNA-seq analysis. The biggest part is to get transcripts sequences as reference for indexing step (kallisto/salmon) from the gff3 file. In following example partial gff3 file, the **exon1** is the same as * ...
transcript-leve gene-level rna-seq transcripts written 4 weeks ago by yifangt860
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Comment: C: strand handling of of reference sequence for index
... Thanks Brian! Is it possible for you to elaborate the indexing procedure for both the forward and reverse strand, technically? What I can guess is the "-" strand is concatenated to the "+" strand to have a single string. Then, how the offsets for each chromosome are distinguished from each other (2 ...
written 10 weeks ago by yifangt860
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strand handling of of reference sequence for index
... Following my [other post,][1] I was wondering how do the short reads mappers (bwa & bowtie2) handle the "-" strand of the reference at the step to build index. As short reads are always in 5'-->3' direction for either strand, but from the mapping result SAM file there are reads mapped to both ...
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Comment: C: How is the FM-index built for multiple entries of a fasta file?
... Hi Rob! Thank you so much for your time answering my tedious questions. I seem to understand the algorithms described in Ben Langmead's notes you mentioned, and I should be more specific with my questions which were actually on the details of implementation. I am studying the C code at this moment t ...
written 5 months ago by yifangt860
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Comment: C: How is the FM-index built for multiple entries of a fasta file?
... In the past week I read some papers and [notes][1]. FM index contains 1) First column of the BWT transformed matrix (F column) which is lexicographically sorted, so only need A/C/T/G four characters; 2) The last column of BWT matrix (L column) which is the same length of the reference genome string( ...
written 5 months ago by yifangt860
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Answer: A: How is the FM-index built for multiple entries of a fasta file?
... Aha, d-cameron, your reply makes me feel better. My question probably only fits into category of beginners on learning the implementation of these important data structures & algorithms, which seem to be quite advanced level, at least to me. Rob's explanation helped, and I am hoping anyone provi ...
written 5 months ago by yifangt860
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How is the FM-index built for multiple entries of a fasta file?
... I was wondering if anybody can explain how the FM-index was created for multiple entries of a sequence file (say, fasta format for a reference genome containing multiple chromosomes). In other words, how does the FM-index distinguish different sequences in a single fasta file? While I was studying ...
software sequence code index written 5 months ago by yifangt860

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