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Recent Replies
Comment: Merging the filename with tsv files for master file
by
smrutimayipanda
▴
20
this is the code which I have written:
import os
import pandas as pd
# Get the list of all the orf.tsv files
orf_tsv_…
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
There are plenty of variants that don't exist in gnomAD - only 759M SNPs (chr-pos-ref-alt) out of a possible 9B. Your question is a bit con…
Comment: Modify the code to take most abundant reads from a cluster and process it.
by
Mohd
▴
40
Hi, Thanks for the help. I am just a beginner and the code was written by someone else, I am trying to modify it for myself. I will try to …
Comment: Hugo_Symbol to Entrez ID
by
GenoMax
134k
Using `EntrezDirect` ([**LINK**][1]):
$ esearch -db gene -query "TSPAN6 [gene] AND human [orgn]" | esummary | xtract -pattern Document…
Comment: Ties in reranked list
by
Hamza
•
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
by
shakyaram079
•
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
by
Y
•
0
I tried the commands you recommended in the bash/command line. When I tried `find "${bam_directory}" -type f -name "*.bam" | xargs samtools…
Comment: Hugo_Symbol to Entrez ID
by
GenoMax
134k
Can you provide some examples of HUGO ID's you are unable to convert?
Comment: Using STAR aligner to build index of hg38
by
GenoMax
134k
GTF file includes gene models/annotation information.
You could also use a program like `salmon/kallisto` with just human transcriptome to…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Pierre Lindenbaum
157k
then test each files.
find "${bam_directory}" -type f -name "*.bam" | xargs samtools quickcheck
file "${reference_gen…
Answer: Ties in reranked list
by
alserg
▴
860
The problem here is not the ties, but that your gene IDs in the pathway list (ensemble human genes) does not match the names of the stats v…
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
•
0
I did not use the space between the `-u` flag and the `-o` flag (the blank line) but I did do what you recommended:
# Run CuffDiff wit…
Answer: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Pierre Lindenbaum
157k
how about simply trying:
```
cuffdiff -u "${annotation_gtf}" \
-o "${output_directory}" \
-b "${reference_genome}" \
-p "${num_th…
Comment: Using STAR aligner to build index of hg38
by
Grace
•
0
Yes, I know also need a GTF file. So the GTF file will include RNA information?
Thanks for your answer!!
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