User: kanwarjag

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kanwarjag810
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Posts by kanwarjag

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Question about mapping motif binding sites to genome location
... I have a naïve but complex question. I used RSAT to get 5 genes -2000 bp upstream sequence of TSS. I used this FASTA file and binding motif (identified from my experiment) in FIMO to see where is the binding site of the identified motif. I know that protein of interest bound very close to TSS. I g ...
genome written 5 weeks ago by kanwarjag810 • updated 1 day ago by Biostar ♦♦ 20
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Ncrna in cufflink analyzed RNA-seq
... I ran RNA- seq analysis through cufflink to cuff diff . I looked in various files but could not see lincRNA/ ncRNA any suggestion in which file I should be looking them Thanks ...
rna-seq written 6 weeks ago by kanwarjag810 • updated 6 weeks ago by Kevin Blighe7.3k
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question about FASTA file extracted from RSAT
... >Homo_sapiens-ENSG00000186115-CYP4F2-ENST00000011989 ENSG00000186115-ENST00000011989; downstream from -2000 to -1; size: 2000; location: chromosome:GRCh38:19:1:58617616:1 15878301 15880300 R I used RSAT tool extract FASTA file. I get the header as above I pretty much understand most of the he ...
chip-seq written 6 weeks ago by kanwarjag810 • updated 6 weeks ago by Pierre Lindenbaum101k
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Motif seq in input seq and genes
... I have identified a chip seq motif. How I can identify occurrences with statistical significance in the number seq that I used to identify such motif. I also want to identify occurrences of this motif in number of genes (names). What tool can be best used for this purpose? Thanks ...
chip-seq written 6 weeks ago by kanwarjag810 • updated 6 weeks ago by vchris_ngs4.2k
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Comment: C: range of fold change in RNA seq
... Did you publish such large FC, any link for your or any such publications. Generally a FC of <100 is reported. Were reviewers OK with such FC? ...
written 6 weeks ago by kanwarjag810
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Comment: C: range of fold change in RNA seq
... Gene grp1 grp1 grp1 grp2 grp2 grp2 1 5.30 5.22 5.14 -3.82 -4.75 -4.49 2 4.87 4.74 4.87 -4.82 -4.75 -4.49 3 6.51 6.24 6.55 -3.24 -1.94 -2.91 4 4.93 4.66 4.83 -4.82 -3.75 -3.49 normalized counts of 4 such genes Grp 1 is treated Grp2 is control ...
written 6 weeks ago by kanwarjag810
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Comment: C: range of fold change in RNA seq
... grp1 is treated induced expression grp2 is untreated control ...
written 7 weeks ago by kanwarjag810
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Comment: A: range of fold change in RNA seq
... I have checked it very thoroughly there is no mistake. Here is snap shot of few such genes raw read from Deseq. Gene grp1 grp1 grp1 grp2 grp2 grp2 A1 1540 1438 1596 2 4 4 A2 2422 2426 2452 28 20 16 A3 1318 1408 1520 8 18 14 A4 2076 2180 2392 6 14 4 A5 994 994 1102 6 4 10 ...
written 7 weeks ago by kanwarjag810
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Comment: C: range of fold change in RNA seq
... Cells were treated with drug for 5 days in a time course experiment. I think reviewers in publication will think it is an artifact, however since such large FC is not in other group comparisons in the same experiment provide an assurance that it real. It is challenging to present such large FC T ...
written 7 weeks ago by kanwarjag810
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range of fold change in RNA seq
... I performed an RNAseq experiment and used DESEq2 to calculate statistical significance of differential expression. When I calculated fold change it ranges from 4 fold to 700 fold. I randomly checked few genes showing very high fold change and observed that mostly all the replicates (three) showed ...
rna-seq written 7 weeks ago by kanwarjag810 • updated 7 weeks ago by theobroma221.0k

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