User: Leila Kian

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Leila Kian10
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10 months, 1 week ago
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k*********@gmail.com

Posts by Leila Kian

<prev • 11 results • page 1 of 2 • next >
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Comment: C: how prepare File containing a mapping of transcripts to genes under Salmon
... yes, I have filtered two column of transcriptome file to be coincident exactly and filterd transcriptome fasta include transcript identifier and Wrap the sequence lines to 80 bases with the tool FASTA Width formatter I couldn't send the error report! because of this probability, I am not Admin! An ...
written 1 day ago by Leila Kian10
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Comment: C: how prepare File containing a mapping of transcripts to genes under Salmon
... thanks for compelet explanations, I tried to do that step by step, finally it will face with error, I dont know why error An error occurred with this dataset: Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ...
written 3 days ago by Leila Kian10
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Comment: C: how prepare File containing a mapping of transcripts to genes under Salmon
... each sequence identifier of transcriptome file is like this: >ENSMUST00000193812.1|ENSMUSG00000102693.1|OTTMUSG00000049935.1|OTTMUST00000127109.1|RP23-271O17.1-001|RP23-271O17.1|1070|TEC| is it correct? ...
written 4 days ago by Leila Kian10 • updated 4 days ago by Jennifer Hillman Jackson25k
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Comment: C: how prepare File containing a mapping of transcripts to genes under Salmon
... Excuse me one more question if I wanted to download these two columns separately on UCSC table browser under Select Fields from mm10.wgEncodeGencodeCompVM16, we have just name Name of gene (usually transcript_id from GTF) and name2 Alternate name (e.g. gene_id from GTF), there is no gene_id to selec ...
written 4 days ago by Leila Kian10
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Comment: C: how prepare File containing a mapping of transcripts to genes under Salmon
... Hello, thank you very much. I meant when I want to to get table include transcript_id and gene_id directly from get data, UCSC Main table browser, under group Gene and Gene predictions, Track UCSC genes, table Known genes, output format secelted fields from primary and ;;; finally send query to Ga ...
written 4 days ago by Leila Kian10
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how prepare File containing a mapping of transcripts to genes under Salmon
... Hi, I don't know exactly which columns should be put for Salmon to convert transcript to the gene on Galaxy? because I made a table include transcript_id and Gene_id by Biomart but Salmon's outputs (quantification and gene_quantification) are same? moreover, I have tried to send a specific table wi ...
deseq2 galaxy salmon rna-seq written 7 days ago by Leila Kian10 • updated 7 days ago by Jennifer Hillman Jackson25k
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(Closed) count and compare microRNA expression value in RNA-Seq data on Galaxy
... Hello, I have a question, I want to count and compare specific microRNA expression value in BAM alignment on Galaxy server, How do I that? thanks in advance ...
galaxy rna-seq mirna microrna count written 4 months ago by Leila Kian10 • updated 4 months ago by Jennifer Hillman Jackson25k
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Comment: C: finding the specific locus of the Bam file
... Hi I have edited the topic and question. yes, that question was what I mean. please don't it close ...
written 5 months ago by Leila Kian10
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Answer: A: Unable to select GTF file from history in featureCounts (Galaxy version 1.6.0.3)
... Hello you could upload GTF file directly again from Tools, get data part and then UCSC main table browser part, after that select every option you want and select GTF from output format and finally send a query to Galaxy. and now you can select GTF from feature-count tools ...
written 5 months ago by Leila Kian10
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How can I get the specific locus of the Bam file
... Hello everyone I want to find a specific locus from bam file on Galaxy, and indeed want to know where is that located, how I do that? thanks in advance ...
bam bedtools intersect galaxy rna-seq written 5 months ago by Leila Kian10

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