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Recent Replies
Answer: Troubleshooting RNA-seq data with DNA contamination
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haibol2017
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We just developed a R package to tackle this problem.
Do you have stranded or unstranded RNA-seq data contaminated with gDNA?
If you wou…
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`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
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Cross posted here (including the code used to make up the counts):
https://support.bioconductor.org/p/9157911/#9157959
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RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
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i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
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He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
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This looks good. Please try with using `--allow-no-sex flag`
plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
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Sofia
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SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2
SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2
SC899361_PC75425_H05 SC899361_PC75425_H…
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Please show me a few lines of phenotype updated .fam file. You can do `head
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Catalog file lists the genomes included. There seem to be 71365 unique items in field 2.
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yes sure !
![enter image description here][1]
[1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
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Greg
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Give it more memory.
~10x more memory, or whatever you can give it,
I had samples that weren't even close to being done after 3.5 da…
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Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
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Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
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