User: bioinfo_ga

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bioinfo_ga0
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Posts by bioinfo_ga

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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 12 weeks ago by bioinfo_ga0 • updated 12 weeks ago by genomax34k
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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 12 weeks ago by bioinfo_ga0 • updated 12 weeks ago by genomax34k
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Comment: C: Zero expression in cuffdiff
... yes this is in case of all the genes ...
written 12 weeks 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 12 weeks ago by bioinfo_ga0 • updated 12 weeks ago by genomax34k
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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 5 months ago by bioinfo_ga0 • updated 5 months ago by jnoble33310
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Comment: C: Reason for multiple mapping of reads ?
... I checked for pseudo genes(homologous) but did not find them , could there be any other possible reason for it ? ...
written 5 months ago by bioinfo_ga0
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Reason for multiple mapping of reads ?
... I have 75x2 (20.77) million reads for Acinetobacter_baumannii sample . I aligned the reads to the reference genome (Acinetobacter_baumannii downloaded from NCBI which has chromosome and two plasmid sequences) with end to end option(bowtie2 program) and got 86.58% reads which aligned concordantly &g ...
rna-seq written 6 months ago by bioinfo_ga0
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Comment: C: Running cufflinks - gtf file not recognised
... can u post the screenshot of the command and error? ...
written 15 months ago by bioinfo_ga0
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Unexplained reads from a genome
... Dear friends, I have six sample ( ~ >36M reads/sample) for ribosomal-profiling. In all the sample, >95% of the reads has adapter sequences as expected. Tophat(default parameters) was used to align the reads against human genome(hg38). For one of the sample had 81.50% alignment and rest had a ...
genome next-gen tophat alignment rna-seq written 15 months ago by bioinfo_ga0 • updated 15 months ago by Biostar ♦♦ 20

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