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Search: Posts Made By: aakriti
Forum: Bioinformatics 08-27-2014, 06:11 AM
Replies: 0
Views: 956
Posted By aakriti
Frequency of a species in HMP database

Hi, I was wondering if anyone knew of a database or table that has information on the frequency of particular species from the different HMP body sites?

I was thinking of using 16S rDNA data that...
Forum: Bioinformatics 08-26-2014, 01:44 AM
Replies: 7
Views: 6,746
Posted By aakriti
Ah yes, my read permissions were wrong. Thank you...

Ah yes, my read permissions were wrong. Thank you for the help!
Forum: Bioinformatics 08-25-2014, 11:22 AM
Replies: 7
Views: 6,746
Posted By aakriti
That doesn't work either :|

That doesn't work either :|
Forum: Bioinformatics 08-25-2014, 11:09 AM
Replies: 7
Views: 6,746
Posted By aakriti
Converting to .fa or .fsa or even .fasta doesn't...

Converting to .fa or .fsa or even .fasta doesn't work and gives me the same errors :\
Forum: Bioinformatics 08-25-2014, 10:35 AM
Replies: 7
Views: 6,746
Posted By aakriti
Bowtie2 and fasta format input

Hello all,

I am trying to make an alignment using Bowtie2 on the following contigs data: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ACGE01#contigs

I downloaded the file that is in the .fsa_nt...
Forum: Bioinformatics 07-18-2014, 03:52 AM
Replies: 13
Views: 2,372
Posted By aakriti
Thank you for all the suggestions! I tried the...

Thank you for all the suggestions! I tried the alignment method suggestions you guys sent me (actually still have to look into BBMap), but am getting the same results (no alignment).

Do you guys...
Forum: Bioinformatics 07-17-2014, 04:10 PM
Replies: 13
Views: 2,372
Posted By aakriti
Ah! Genomax, you took the words out of my mouth :P

Ah! Genomax, you took the words out of my mouth :P
Forum: Bioinformatics 07-17-2014, 04:10 PM
Replies: 13
Views: 2,372
Posted By aakriti
OKay I can write a script to try that. Do you...

OKay I can write a script to try that. Do you think it would be possible to use the query sequences as the reference and try to align my gene of interest to that? Or would that not work (still trying...
Forum: Bioinformatics 07-17-2014, 04:04 PM
Replies: 13
Views: 2,372
Posted By aakriti
Do you mean dividing the query sequences further?...

Do you mean dividing the query sequences further? I believe this could be the case since the reference sequence is just one gene.
Forum: Bioinformatics 07-17-2014, 02:09 PM
Replies: 13
Views: 2,372
Posted By aakriti
Thanks for the response! Where can I set the...

Thanks for the response! Where can I set the parameters for the alignment? Is it in the Bowtie2_build file?
Forum: Bioinformatics 07-17-2014, 07:49 AM
Replies: 13
Views: 2,372
Posted By aakriti
Help with Bowtie2

Hi all!

I am currently working on a project where I am trying to align assembled scaffolds from the Human Microbiome Project to a gene sequence (agaA from C. striatum). I am having trouble with...
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