User: hirahameed222

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Posts by hirahameed222

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How to create table counts for Ballgown after performing StringTie for Estimateion transcript abundance.?
... I am using HISAT2 ,Stringtie & Ballgown for differential expression analysis of wheat RNA-seq data. According to this Protocol in a Step **Estimate transcript abundances and create table counts for Ballgown:** we use this Command and GTF files are produced as output result. Command: `$ stringtie ...
R rna-seq written 12 days ago by hirahameed2220
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Question: How And From Where Do I Download Reference Genome For BreadWheat?
... i am not much expert of the Analysis and Transcrpt aseembly work. i actually don't know actually how to download the reference genome for bread wheat *triticum aestivum* and from where. please can anybody guide me ? I need this for indexing with HISAT2. ...
gene assembly sequencing genome written 17 days ago by hirahameed2220 • updated 17 days ago by genomax64k
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Comment: C: STRINGTIE WARNING: no reference transcripts were found for the genomic sequences
... Can you please suggest the suitable Reference genome for wheat and Gtf/gff3 file for wheat to avoid such error . I would be very thankful if you can help me in providing these (links) since i tried and tested many RefGenomes (even few top level too) but everytime i got the same error. ...
written 17 days ago by hirahameed2220
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STRINGTIE WARNING: no reference transcripts were found for the genomic sequences where reads were mapped
... Hi everybody! I am using RNA-Seq protocol for identifying differentially expressed gene in RNASEQ data of 6 wheat varieties. I am following this protocol https://www.nature.com/articles/nprot.2016.095. My Reference genome source is as under. I downloaded the assembled sequences from ftp://ftp.ncbi ...
assembly rna-seq written 17 days ago by hirahameed2220
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how to Obtain/fetch the Sequnece of Gene by RNA-SEQ data (Wheat)
... I have been trying for a long time to look for gene DRO1, RPKI of wheat from my sequenced Wheat Data. I am using the new tools like Hisat2 for Aligning RNA-SEQ reads to Reference Genome and finally i got Sorted Bam files. (i have used String tie to Assemble transcripts for each sample and Merge tra ...
gene next-gen rna-seq sequencing written 26 days ago by hirahameed2220
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Comment: C: How to merge annotation file(gtf) from different souce
... Can you please help me, How can i Download Reference genome of Wheat (triticum aestivum) as index for mapping (with RNA-seq) by HISAT2. ...
written 9 weeks ago by hirahameed2220
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Comment: C: Reference genome for wheat/ Triticum aestivum
... Can you please help me, How can i Download Reference genome of Wheat (triticum aestivum) as index for mapping (with RNA-seq) by HISAT2. ...
written 9 weeks ago by hirahameed2220
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(Closed) Reference genome of Wheat (triticum aestivum)
... How can i Download Reference genome of Wheat (triticum aestivum) as index for mapping by HISAT2 with RnaSeq Data. ...
assembly next-gen rna-seq alignment hisat2 written 9 weeks ago by hirahameed2220 • updated 9 weeks ago by lieven.sterck4.2k

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