User: hudiejie

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hudiejie0
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Singapore
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2 years, 9 months ago
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Posts by hudiejie

<prev • 13 results • page 1 of 2 • next >
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Comment: C: about 'IGV view'
... Hi Hans-Rudolf, Thank you very much for your reply and I can find a lot of existed database to choose as a database. And besides, I can add in new database/build if the genome which is not in the database list as a reference. : ) ...
written 2.8 years ago by hudiejie0
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about 'IGV view'
... Hi, I wanted to display my bowtie or cuffmerge result in IGV view, the sentence came out: 'The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.' How could I do to add a genome to the f ...
igv written 2.8 years ago by hudiejie0 • updated 2.8 years ago by Hotz, Hans-Rudolf1.7k
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How to set Trinity parameter:--jaccard_clip
... Hi all, Does any know how to set --jaccard_clip in trinity? Seems there is no option for this, but for my sample, it is fugal which is needed this parameter: 'If your transcriptome RNA-seq data are derived from a gene-dense compact genome, such as from fungal genomes, where transcripts may often ...
trinity written 3.1 years ago by hudiejie0 • updated 3.1 years ago by Jennifer Hillman Jackson23k
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Tophat can run negative r
... Regarding to Mean Inner Distance between Mate Pairs, I tried run ~1000000 reads twice: (1) if r='fragment length - pair end reaength'= 280-100*2=80 bp. I have got 350,000 lines of tophat: accepted hits. (2) if r='fragment size - paired end read length - adaptor length = = 280 - 202 - 121(58bp+63 ...
tophat written 3.1 years ago by hudiejie0 • updated 3.1 years ago by Jennifer Hillman Jackson23k
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Answer: A: How can I use galaxy to run RNA-seq analysis without reference seqence?
... Hi Fubar, Thank you for your reply. Just add sth: The raw data has pass the FastQC test and has been trimmed without adapters. And the low mapping rate is double confirmed by the sequencing center BI team. Still open to any other explanations for the low mapping rate. I have a local Galaxy insta ...
written 3.1 years ago by hudiejie0
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How can I use galaxy to run RNA-seq analysis without reference seqence?
... Recently I have got my RNA-seq data of a fungal species under several treatments. There are refseq files (fasta, gbff and bbs) available in NCBI, but the alignment/mapping rate is quite low (3-4%). So here I have several questions: 1.Based on NCBI refseq, there is no annotation file available. For ...
analysis rna-seq refseq alignment referencedata written 3.1 years ago by hudiejie0
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Comment: C: Where to find Bowtie2 output stderr filehandle?
... I found it! Thanks a lot! ...
written 3.2 years ago by hudiejie0
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Answer: A: How to set 'mean inner distance' for paired-end reads?
... Hi all, I have check with Tophat team, but since now there is no any replies. I have found this (url: http://ccb.jhu.edu/software/tophat/faq.shtml#mate_inner_dist): 'If you want to find a good approximation of this distance for your reads you can try running Bowtie2 on a small sample (subset) of ...
written 3.2 years ago by hudiejie0
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Where to find Bowtie2 output stderr filehandle?
... Dear all, I want to find the alignment rate as suggested in bowtie2 "standard error" ("stderr") file, but after running bowtie2, there is only one bam file of aligned reads. where can I find the info like this: 20000 reads; of these: 20000 (100.00%) were unpaired; of these: 1247 (6.24%) aligned ...
bowtie2 written 3.2 years ago by hudiejie0 • updated 3.2 years ago by Bjoern Gruening4.8k
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Comment: C: How to set 'mean inner distance' for paired-end reads?
... The error:   Settings: Output files: "/tmp/5447.1.batch/tmpqSneiZ/dataset_1720.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default Max buck ...
written 3.2 years ago by hudiejie0

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Scholar 3.1 years ago, created an answer that has been accepted. For A: How can I use galaxy to run RNA-seq analysis without reference seqence?

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