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Recent Replies
Comment: Ties in reranked list
by
Hamza
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0
I had actually accidentally used ranks instead of Entrez gene ids (but switched later to human Ensembl gene ids). However, without your com…
Comment: Hugo_Symbol to Entrez ID
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shakyaram079
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0
Yes sure. These are all gene IDs BZRAP1, C19orf60, TCEB3 and so on.
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
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Y
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I tried the commands you recommended in the bash/command line. When I tried `find "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID
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GenoMax
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Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38
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GenoMax
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GTF file includes gene models/annotation information.
You could also use a program like `salmon/kallisto` with just human transcriptome to…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
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Pierre Lindenbaum
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then test each files.
find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck
file "${reference_gen…
Answer: Ties in reranked list
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alserg
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The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
•
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I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended:
# Run CuffDiff wit…
Answer: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
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Pierre Lindenbaum
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how about simply trying:
```
cuffdiff -u "${annotation_gtf}" \
-o "${output_directory}" \
-b "${reference_genome}" \
-p "${num_th…
Comment: Using STAR aligner to build index of hg38
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Grace
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Yes, I know also need a GTF file. So the GTF file will include RNA information?
Thanks for your answer!!
Comment: STAR Intron Motif Script Gives Segmentation fault Error
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Y
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I will try and figure it out on my own given what you all have mentioned. Thank you for your time.
Comment: Using STAR aligner to build index of hg38
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Amitm
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Have you gone through the manual [here][1]. In addition to the genome fasta file, you would also need a GTF file (of gene annotations) to b…
Comment: Highly inflated p-values in GWAS by regenie
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4galaxy77
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You still definitely need to include principle components as covariates, even if your data is from the same ethnicity. Not including those …
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Christophe
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Hi,
D-genies is using minimap2 to align both genomes and minimap2 is chaining local alignments to produce a global one. If the SV are sm…
Comment: Ties in reranked list
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Hamza
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In this case there are no results in my fgsea object unfortunately
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