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Manifest and off target

Link: https://www.biostars.org/p/395763/

FREEThe % of off-target reads is just a metric. Usually reads in this region are not removed. Your manifest file should list all region that where captured/enriched during library prep. A high % of off-target reads would indicate that the enrichment was not ideal. ... See Details

Recommended cutoff for FDR - 0.05 or 0.1

Link: https://www.biostars.org/p/209118/

FREEThink about what "false discovery rate" actually means. Whatever your FDR cutoff, that's the proportion of genes that you call as differentially expressed that you expect really aren't differentially expressed. So if you call 500 genes as DE with an FDR cutoff of 0.1, you expect 50 of them to be false positives. ... See Details

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Link: https://www.biostars.org/?sort=creation&limit=all%20time&q=malanaz.com/giay-cao-got-nu-cao-cap-sale-off-35-malanaz/

FREEYes, this is normal and expected. Please use google / the biostars search function next time befo... ... See Details

Biostar Forum

Link: https://www.biostars.org/p/183772/

FREESo you can try to run the analysis at different -q values (0.05,0.01) while keeping the --broad-cutoff as 0.1 or you can set the similar same value of q-value cut-off as the --broad-cut-off say 0.05 or 0.01. Once you have the peaks for all these runs you can simply count the … ... See Details

Biostar Forum

Link: https://www.biostars.org/p/236523/

FREEI have retrieved different datasets (supplementary raw data as well as in SRA format) from GEO, NCBI related to particular virus. I am interested to study the differential gene expression and further downstream analysis relating with various celllular pathways. ... See Details

Mutect2 gets different results when I change the

Link: https://www.biostars.org/p/256864/

FREEI use mutect2 of GATK 3.6 and GATK 3.7 to call variant. I know there is a downsampling in mutect2 which has an important influence on the result. ... See Details

Biostar Forum

Link: https://www.biostars.org/p/112410/

FREEOff topic:How to get FASTA sequences from GI number . 0. Entering edit mode. 6.5 years ago. ste.colombo • 0 @stecolombo-13534. Hey guys I need help. I need to download a large amount of FASTA sequences from a set of GI number. Is there any script to do this?? ... ... See Details

Biostar Forum

Link: https://www.biostars.org/p/103855/

FREEEDIT: Just had to order the data frame by adjusted p-value before plotting!I'm leaving this up in case someone runs into a similar problem. I'm using DESeq to analyze count data from RNASeq of maize and fungus during pathogenesis. ... See Details

Biostar Forum

Link: https://www.biostars.org/p/459608/

FREEWith small reads, you're better (and faster) off to use an aligner/mapper such as bwa or bowtie(2). ADD REPLY • link 6 months ago by cschu181 ♦ 2.6k 0. Entering edit mode. 6 months ago. Richard • 580 @richard-4015. Are your reads in fastq format? If so it sounds as though you ... ... See Details

Biostar Forum

Link: https://www.biostars.org/p/322029/

FREEglmTreat does not work with a strict cut off, but uses an alternative hypothesis testing. In a normal test the hypothesis is 0 (FC) difference, but with glmTreat you test directly whether there is a 5 fold change. If this is not the case the 5 fold change is not significant (even if you find logFC > 2.8). ... See Details