User: mmacd

gravatar for mmacd
mmacd20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
1 year, 4 months ago
Joined:
4 years, 7 months ago
Email:
m****@udel.edu

I am a Systems Biology/Bioinformatics PhD graduate student at University of Delaware.

Posts by mmacd

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Maker Output: transcript names
... Hi Vijay, I had sent the same question to the Maker email list awhile back and go the following response: "They are different genes because their ID’s are different. The numbers are meaningless, they are just iterators to make sure the ID’s are unique" Hopefully this helps! ...
written 16 months ago by mmacd20
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Answer: A: MUGSY install troubleshoot
... Was a solution ever found to this problem? I am getting the same error even though I have 'run source mugsyenv.sh' and 'echo $MUGSY_INSTALL' returns the path to my mugsy executable. ...
written 21 months ago by mmacd20
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Comment: C: Downloading all introns from Ensembl for Grch37
... Changing the while loops to foreach seemed to do the trick. ...
written 2.9 years ago by mmacd20
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Comment: C: Downloading all introns from Ensembl for Grch37
... Do you know if the coordinates for Hg19 and Grch37 the same? Since that gives me intron coordinates based on Hg19. If they are the same, then i think that would have worked. ...
written 2.9 years ago by mmacd20
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Comment: C: Downloading all introns from Ensembl for Grch37
... Oh ignore the post before. If I use port 3337 with no db version specified, I get introns from GRCh37. Thank you both so much for your help! I am having an additional issue now. My code seems to hang on the first canonical transcript's intron. It prints it multiple times and then hangs. Here the ...
written 2.9 years ago by mmacd20
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Comment: C: Downloading all introns from Ensembl for Grch37
... So I am using the same code as I posted above but with port 3337 and homo_sapiens_core_84_37 as the db. I am using the newest API. However, now im getting the following error: -------------------- WARNING ---------------------- MSG: Human is not a valid species name (check DB and API vers ...
written 2.9 years ago by mmacd20 • updated 2.9 years ago by genomax68k
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Comment: C: Downloading all introns from Ensembl for Grch37
... Tried that too, since keeping UCSC and then converting would have been much easier, but only a very small portion (less than 10%) of my UCSC ids could be converted! The table browser is nice and easy to use, I just hope they get an updated KnownToEnsembl table soon where more ids can be converted. ...
written 2.9 years ago by mmacd20
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Comment: C: Downloading all introns from Ensembl for Grch37
... I want the introns associated with ENSEMBL ids specifically, not UCSC ids (this is actually what we were using originally but UCSC ids are hard to convert to other ids or to give them functional meaning, so we are trying to move away from using them). Thanks though! ...
written 2.9 years ago by mmacd20
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Downloading all introns from Ensembl for Grch37
... I was wondering if anyone could give me advice on acquiring all introns from human Grch37 from Ensembl? I can get the introns from human Grch38 through Perl API using the following code: use strict; use warnings; use Bio::EnsEMBL::Registry; use Bio::EnsEMBL::Utils::SeqDumper; ...
ensembl intron introns homo sapiens perl api written 2.9 years ago by mmacd20 • updated 2.9 years ago by igor7.7k
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Maker Output: transcript names
... Hi all, I have a question about the output of Maker. After running fasta_merge on the Maker results, I get the fasta files which include all the gene annotations from all the different contigs in the assembly. In the transcript file, I get headers such as the two below: maker-Contig206-snap-gene-3 ...
genome annotation maker written 3.2 years ago by mmacd20

Latest awards to mmacd

Popular Question 2.2 years ago, created a question with more than 1,000 views. For Converter for GFF file downloaded from NCBI to GTF
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Determining the accuracy of a "merged" genome assembly
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

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