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Answer: Adding CB tag to bam file
by
Maria
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Sorry for the delay in my answer, I got sidetracked.
I am using
```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE```
bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
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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):
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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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bk11
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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…
Comment: How to convert plink files to Hapmap Format
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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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Comment: GEMMA GWAS how to specify factor or numerical for covariates
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Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
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Catalog file lists the genomes included. There seem to be 71365 unique items in field 2.
2 Bacteria WP_000018326.1 4459…
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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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