User: j_susat

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j_susat40
Reputation:
40
Status:
New User
Location:
Kiel
Last seen:
1 year, 7 months ago
Joined:
2 years, 10 months ago
Email:
j******@web.de

Posts by j_susat

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Sam Format Optional Fields Specification
... Thank you. I was searching at the wrong place then :) ...
written 21 months ago by j_susat40
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Comment: C: Sam Format Optional Fields Specification
... Sorry. I will add the information. ...
written 21 months ago by j_susat40
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Sam Format Optional Fields Specification
... Hey there, I currently try to find out what the flag XA:Z: means. I looked through this PDF [optional field specification][1] but it just says that tags starting with X are reserved for end users. So does anyone know what this flag means? Here is one example of my sam file. This is a result of a m ...
alignment sam written 21 months ago by j_susat40 • updated 21 months ago by Devon Ryan91k
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Lost in the Matrix (BlastX issues)
... Hey there, I' am currently struggling with the selection of the right matrix and some thoughts from you would be very helpful. As I' am a guy from the ancient DNA field the samples that I have to deal with contain mostly of short reads ranging from 40 to 150 bases. And I'am interested in finding ...
blast written 2.4 years ago by j_susat40
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Comment: C: Issue with installing bowtie2
... I guess you could download the Bowtie2 source code and then change the makefile so that it points to your location of the TBB library. But at the moment I'am not sure what to change. And by the way even without the TBB library Bowtie2 is a very fast aligner. But it always depends on what you are g ...
written 2.6 years ago by j_susat40
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Answer: A: Issue with installing bowtie2
... I had the same error just a few minutes ago. In the newest Version Bowtie2 seems to need the TBB Library for better perfomance but it is missing on your cluster. However there is a way to compile it without the need of the TBB Library as stated here: [Bowtie Homepage][1] However if you want to use ...
written 2.6 years ago by j_susat40
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Answer: A: How to download all the parasite protein data from NCBI?
... Hello, if you just want to Download all the bacterial proteins from NCBI you could use Entrez Direct: [Click Here][1] Here is some small example which could do the job (restricted to refseq) esearch -db protein -query "bacteria [ORGN] AND refseq [filter]" | efetch -format fasta > bacterial ...
written 2.6 years ago by j_susat40
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Comment: C: Identify all proteins smaller than 150 AA
... You could try this: esearch -db protein -query "Staphylococcus aureus [ORGN] AND refseq[filter]" | efilter -query "40:150 [SLEN] AND secretion [ALL]" | efetch -format fasta > aureus_protein_test it is a bit more stringent due to refseq and secretion restricitons. I guess there is a better ...
written 2.7 years ago by j_susat40
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Answer: A: Identify all proteins smaller than 150 AA
... Ok, I guess since you tagged database and query it is about downloading from a database. So here is an Idea how you could do that with Entrez Direct: esearch -db protein -query "Staphylococcus aureus [ORGN]" | efilter -query "40:150 [SLEN]" | efetch -format fasta > aureus_protein_test In ...
written 2.7 years ago by j_susat40
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Comment: C: Identify all proteins smaller than 150 AA
... What do you mean with Identify? You want to download them from for example from NCBI for different organisms or do you mean something else? ...
written 2.7 years ago by j_susat40

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Scholar 2.6 years ago, created an answer that has been accepted. For A: How to download all the parasite protein data from NCBI?

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