User: marlenejensen

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Posts by marlenejensen

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Seqkit - change regex for parsing ID
... Interesting! Repeating your commands using a test file worked for me as well so it seems to be an issue with the format of my input database. Thank you! ...
written 2 days ago by marlenejensen20
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Comment: C: Seqkit - change regex for parsing ID
... Oh I see. Well, the sequences are different in my case. See example below. >Host_331002_c0_seq1 95 1381 2 + MXETIKQVVVDEVSLLFVKPREXXYNFYCTEKELNKYXRDLCTGETMTGR VIIVTGASSGLGYETARYLCEGGNDVILACRDEEKAKRAIDRIKQQNPNA LATYMHLDLSSLESVRKFVDEFHATGKKLHVIVNNAGLALNFKDIKRQYT ADGFELTIGTNHLGP ...
written 2 days ago by marlenejensen20 • updated 2 days ago by cpad011213k
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Seqkit - change regex for parsing ID
... Hi guys, I am trying to use seqkit rmdup to remove duplicated sequences from my protein fasta files. However, it's only the accession numbers which are duplicated and not the description or sequences. See example below. Host_331002_c0_seq1 95 1381 2 + Host_331002_c0_seq1 1873 2112 1 + So ...
duplicates database seqkit regex written 6 days ago by marlenejensen20
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Comment: C: Bbmap filterbyname.sh to extract sequences out of a fasta file - wrong output
... Great, thanks for your advice! ...
written 7 months ago by marlenejensen20
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Comment: C: Bbmap filterbyname.sh to extract sequences out of a fasta file - wrong output
... The format of the accessions is varies a lot, depending on how the data was generated. e.g. >Delta1_2004206643 orf2_0004_16 Aldehyde ferredoxin oxidoreductase [O.algarvensis Delta1] # COG COG2414(C) >Host_265335_c1_seq1_5 [136 - 2] (REVERSE SENSE) len=239 path=[217 0-135 353 136- ...
written 7 months ago by marlenejensen20 • updated 7 months ago by genomax83k
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Bbmap filterbyname.sh to extract sequences out of a fasta file - wrong output
... Hi guys, I wanted to extract specific sequences out of a fasta file based on its accession number. Therefore I used bbmap filterbyname.sh and at the first view it looked perfectly fine. I run this command: filterbyname.sh in=DB.fasta out=SequencesOfInterest.fasta names=Accessions_DB.txt includ ...
bbmap sequence extraction written 7 months ago by marlenejensen20 • updated 7 months ago by WouterDeCoster43k
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Comment: C: Manipulate output join command linux
... Yes, I am bit confused as well since it worked fine for me in the past,...I checked for chars but couldn't find anything. But I will try to convert back to linux, thanks. I tried the paste command and it starts printing the content of the two files. Is that what it should do? Thanks again for the ...
written 7 months ago by marlenejensen20
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(Closed) Manipulate output join command linux
... Hey guys, I used the join command to join two tab separated text files on a common field. This worked perfectly fine except for the output. I expexted something like: File A: 1 A 2 B 3 C File B: 1 a 2 B 3 C New file: 1 Aa 2 Bb 3 C ...
linux command line join command standard output written 7 months ago by marlenejensen20 • updated 7 months ago by Biostar ♦♦ 20
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Database annotation for metaproteomics
... Hey all, I am using a metaproteomic database for the gut microbiome of mice which I found online http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP. Unfortunately, the accession numbers and protein descriptions are not really helpful for taxonomic analyses since they are like this: ...
next-gen written 12 months ago by marlenejensen20 • updated 12 months ago by RamRS27k
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Comment: C: What is the best/most accurate protein secretion signal predictor?
... Yes, right....I forgot that. I have bacteria sequences and want to look at pathway IV.. ...
written 15 months ago by marlenejensen20

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Popular Question 6 months ago, created a question with more than 1,000 views. For How to extract pattern matching sequences from a fasta file?

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