User: testtube

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Posts by testtube

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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... Quite frankly, I used these parameters by default now. I have spent some time over different projects with various parameters and when I used these, which come from the ENCODE protocols, I systematically get higher *uniquely mapped reads*. I tend to simply move on when they give me *uniquely mapped ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... Thank you for your suggestion. The previous correlation were of FPKM. It might not have been ideal. I get the following correlations: Read counts >control_salmon treated_salmon control_star_salmonquant treated_star_salmonquant control_star treated_star control_salmon 1.00 treated_salmon 0.9 ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... Control_1 - lib_format_counts.json (all are similar) >"expected_format": "ISR", "compatible_fragment_ratio": 1.0, "num_compatible_fragments": 54316218, "num_assigned_fragments": 54316218, "num_frags_with_concordant_consistent_mappings": 49773378, "num_frags_with_inconsistent_or_ ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... Thanks you for your help. Looking at the raw count I'm even more confused. DE in salmon but not STAR (featureCount raw count) > treated_1 treated_2 treated_3 control_1 control_2 control_3 > SALMON DE gene_A 237.813 125.654 258.512 634.975 322.316 458.968 > STAR gene_A 1400 1017 18 ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... They are FPKM ` fpkm(dds)` ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... DE in salmon but not STAR > gene_name gene_biotype treated_1 treated_2 treated_3 control_1 control_2 control_3 baseMean log2FoldChange lfcSE stat pvalue padj > SALMON DE gene_A protein_coding 22.46318 19.45674 8.177063 6.213502 3.343609 3.186051 399.5247 1.974991 0.4897088 4.032992 5.51E-0 ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... That's my main problem, the significant DE (baseMean >= 1, abs(l2FC) >= 1, padj <= 0.05) lists are very different. ![DE signif][1] [1]: https://i.ibb.co/p2XX6HB/DE-signif-salmon-vs-star.png ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... Thanks. The correlation between the average of the 3 "control" replicates is 0.53 and the correlation between the average of the 3 "treated" replicate is 0.55. Lower than I would have expected. I'm not sure what you mean by "projected to the transcriptome". ...
written 5 weeks ago by testtube0
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Comment: C: DEseq2 results differs greatly when comparing output from STAR/featureCounts and
... Thanks, this makes sense. But for such cases, which list can I trust, or at least should prefer as the basis for further biological validation and experiments? ...
written 5 weeks ago by testtube0
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DEseq2 results differs greatly when comparing output from STAR/featureCounts and Salmon
... I have a standard RNA-seq dataset, 3 replicates of treated and control. I have obtained the read counts according to 2 different pipelines, first with STAR and featureCounts (with ENCODE preferred options) and second with Salmon. **First pipeline (STAR -> featureCount -> DEseq2)** STAR \ ...
deseq2 salmon star rna-seq written 5 weeks ago by testtube0 • updated 5 weeks ago by Rob4.0k

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