User: bioinfo_ga

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bioinfo_ga0
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Posts by bioinfo_ga

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Comment: C: duplicate/invalid 'transcript' feature in cuffmerge
... For all the features of a given transcript we have the same name. ...
written 7 months ago by bioinfo_ga0
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Comment: C: duplicate/invalid 'transcript' feature in cuffmerge
... Yes the same gff was used for analysis ...
written 7 months ago by bioinfo_ga0
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Comment: C: duplicate/invalid 'transcript' feature in cuffmerge
... grep "Ma03_t01040.3" gives the following result > chr03 manual_curation exon 836456 836913 . - . transcript_id > "Ma03_t01040.3"; > chr03 manual_curation exon 837103 837214 . - . transcript_id > "Ma03_t01040.3"; > chr03 manual_curation exon 837626 ...
written 7 months ago by bioinfo_ga0
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duplicate/invalid 'transcript' feature in cuffmerge
... Hi !! I am doing alignment against banana genome using hisat downloaded from ( http://banana-genome-hub.southgreen.fr/). Further i used cufflinks (2.2.1)for expression estimation which runs fine but in cuffmerge step it gives the following error "duplicate/invalid 'transcript' feature ID=Ma03_t01040 ...
rna-seq written 7 months ago by bioinfo_ga0
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Gene elongation observed in rnaseq analysis
... I have used tuxedo pipeline for rnaseq analysis of mouse samples. Reference and gtf(mm10) were downloaded from ucsc. In my cuffdiff results for one gene GAD1 i am observing gene elongation as its original coordinates are 70562129-70602014 and the coordinates observed in cuffdiff are 70489940-705633 ...
rna-seq written 11 months ago by bioinfo_ga0
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Comment: C: Zero expression in cuffdiff
... 1) Cufflinks is giving me non zero expression values. 2) I have checked with Reference.gff as well as converted it to gtf format, both gave the same result. 3) Reference and gff are same. Sam file first five lines are as follows: NS500223:206:HJ7TTBGXY:3:11605:17662:2653 73 10 2 ...
written 15 months ago by bioinfo_ga0 • updated 14 months ago by genomax57k
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Comment: C: Zero expression in cuffdiff
... Hisat was used for alignment, and further sorted sam was used for cufflinks Cufflinks: cufflinks -G Reference.gff -o Cufflinks/Set2 -p 25 --library-type fr-firststrand --upper-quartile-norm 1A_s.sam Cuffdiff: cuffdiff -u -p 25 --library-type fr-firststrand --total-hits-norm -o Cuffdiff/ ...
written 15 months ago by bioinfo_ga0 • updated 14 months ago by genomax57k
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Comment: C: Zero expression in cuffdiff
... yes this is in case of all the genes ...
written 15 months ago by bioinfo_ga0
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Zero expression in cuffdiff
... I have done reference alignment using tophat pipeline on 150*2 reads. For expression calculation i am using Cuffdiff , however i am getting 0 expression (as given below) for control as well as treated samples. test_id : TCONS_00000001 gene_id : XLOC_000001 gene ...
cuffdiff rna-seq written 15 months ago by bioinfo_ga0 • updated 15 months ago by genomax57k
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Prediction of TSS from tuxedo pipeline
... I have 22Million (150*2) human transcriptome reads. I have performed reference alignment using tuxedo pipeline (Tophat followed by Cufflinks).I need to calculate transcription start site (TSS) in my aligned transcripts and how to calculate position of TSS with respect to proximal and distant promote ...
tuxedo rna-seq tss written 17 months ago by bioinfo_ga0 • updated 17 months ago by jnoble33320

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