298
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122
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28k
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29 follow
146
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70
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46k
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20 follow
updated 26 days ago by
Raheleh
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260
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written 5.8 years ago by
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86k
162
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64
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80k
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39 follow
170
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41
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91k
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27 follow
100
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38
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28k
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34 follow
updated 24 days ago by
Jeremy Leipzig
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written 9.9 years ago by
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3.6k
105
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26
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40k
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updated 5 days ago by
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written 10.7 years ago by
henryvuong
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810
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25
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updated 10 days ago by
Ram
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written 7.5 years ago by
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250
35
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23
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27k
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updated 21 days ago by
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40
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written 2.2 years ago by
Michal Nevo
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110
33
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23
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18k
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updated 10 days ago by
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30
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written 5.5 years ago by
JJ
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660
18
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22
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Tutorial:
Create de novo repeat library
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21
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2.8k
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81
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21
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40k
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15 follow
updated 9 days ago by
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180
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written 9.6 years ago by
pristanna
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750
2
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20
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1.5k
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10
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18
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3.1k
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75
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18
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2.0k
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11 follow
8
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17
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1.1k
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Roop
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0
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written 18 days ago by
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16
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1.8k
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36
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16
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28k
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15
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3.3k
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14
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26k
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20
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written 7.3 years ago by
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260
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19
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14
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vincenthus
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124
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579
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280
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30
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677
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475
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4
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12
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3.4k
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updated 10 days ago by
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30
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written 3.4 years ago by
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4.2k
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updated 3 days ago by
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40
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written 7.7 years ago by
fi1d18
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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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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 "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID
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GenoMax
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Can you provide some examples of HUGO ID's you are unable to convert?
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GTF file includes gene models/annotation information.
You could also use a program like `salmon/kallisto` with just human transcriptome to…
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Pierre Lindenbaum
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then test each files.
find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck
file "${reference_gen…
Answer: Ties in reranked list
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alserg
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The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
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Y
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I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended:
# Run CuffDiff wit…
Answer: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
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how about simply trying:
```
cuffdiff -u "${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!!
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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.
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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…
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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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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…
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In this case there are no results in my fgsea object unfortunately
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