User: worarado.kan

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worarado.kan10
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Posts by worarado.kan

<prev • 27 results • page 1 of 3 • next >
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String Tie with DESeq2
... When I run DESeq2 and showed error. Could you tell me what should I edit? countData <- as.matrix(read.csv("genes.count.matrix3.csv", row.names="gene_id")) Error in data[[rowvar]] : attempt to select less than one element in get1index this is my csv file Fuji_1 Fuji_2 Fuji_3 ...
rna-seq written 5 months ago by worarado.kan10 • updated 5 months ago by ATpoint36k
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Comment: C: Tophat2 command analysing
... Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (GDDH13_1-1_formatted.2.bt2.*.bt2l) [hscience@localhost Tophat2]$ it always showed error. I dont understand why can not find index ...
written 5 months ago by worarado.kan10
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Comment: C: Tophat2 command analysing
... Thank you so much for information ...
written 6 months ago by worarado.kan10
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Comment: C: Tophat2 command analysing
... Thank you for your message ...
written 6 months ago by worarado.kan10
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Tophat2 command analysing
... I try running mapping to reference using tophat -cluffink after I run bowtie2-build I get GDDH13_1-1_formatted.1.bt2 GDDH13_1-1_formatted.2.bt2 GDDH13_1-1_formatted.3.bt2 GDDH13_1-1_formatted.4.bt2 GDDH13_1-1_formatted.rev.1.bt2 GDDH13_1-1_formatted.rev.2.bt2 Next I have to run tophat2 but I have a ...
rna-seq written 6 months ago by worarado.kan10
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Comment: C: how to change gtf to fasta file of cufflink, gffread
... Yes I mean head of fasta file because next step I have to joint fasta file with genes.exp.cuffdiff file, so I need the same ID Could you help how to use command? sorry Im new for this analysis Thank you so much Kanjana ...
written 9 months ago by worarado.kan10
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Comment: C: Cufflinks gffread utility
... In gffread, if I need only TCONS_00033653 and gene_id "XLOC_028018 ID. what is command I should use? Actually, I used gffread -w ECvsEL_transcript.fasta -g v.corymbosum_GDV_reftransV1.fasta EC_vs_EL.gtf But I get only TCONS_00033653 ID Thank you so much kanjana ...
written 10 months ago by worarado.kan10
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how to change gtf to fasta file of cufflink, gffread
... Dear all, I would like to change gtf file to fasta file. In gffread, if I need only TCONS_00033653 and gene_id "XLOC_028018 ID. what is command I should use? My gtf file is v.corymbosum_GDV_reftransV1_0039461 Cufflinks exon 1171 1309 .- . gene_id "XLOC_028018"; transcript_id "TCONS_00033 ...
software error alignment rna-seq sequencing written 10 months ago by worarado.kan10 • updated 9 months ago by kristoffer.vittingseerup3.4k
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using gffread for change GFF file to GTF file
... Hello everyone, I try to change GFF file to GTF for analysing in HISAT. Why when I run following this command; gffread Blueberry.gff -T -o Blueberry.gtf Showed this error GFF Error: overlapping duplicate gene feature (ID=CUFF.71) GFF Error: overlapping duplicate gene feature (ID=CUFF.168) GFF ...
next-gen rna-seq sequencing written 2.2 years ago by worarado.kan10
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How to change scaffold.fasta file or scaffold.bed file to GTF file?
... Hello everyone, I have a problem about changing scaffold.fasta file or scaffold.bed file to GTF file. I would like to analyse using HISAT,stringtie and ballgown that required GTF file of reference. I try to do follow these website but still not complete. https://www.biostars.org/p/64346/ http://o ...
assembly next-gen rna-seq written 2.2 years ago by worarado.kan10

Latest awards to worarado.kan

Popular Question 2.1 years ago, created a question with more than 1,000 views. For using gffread for change GFF file to GTF file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to convert original BED file to a GTF ?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to build index of reference scaffold.fasta using bowtie?

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