User: jamie.pike

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jamie.pike60
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@jamielpike56
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j*********@warwick.ac.uk

Posts by jamie.pike

<prev • 55 results • page 1 of 6 • next >
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Comment: C: Is there a way to produce/convert nhmmer output to a bed file?
... No, I haven't heard of it! I'll take a look at it. Thank you :) ...
written 6 days ago by jamie.pike60
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Comment: C: Is there a way to produce/convert nhmmer output to a bed file?
... @Fatima, thank you. I'm trying to find a transposable element on specific scaffolds so there is variation in strandedness. Perhaps I will try annotating first using hmmer. Thank you for your help. Ps I have found also that --tblout will provide location information and strandedness. ...
written 6 days ago by jamie.pike60
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Comment: C: Is there a way to produce/convert nhmmer output to a bed file?
... @Fatima, Strand information would be useful also but I can't work out where it is? ...
written 6 days ago by jamie.pike60
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Comment: C: Is there a way to produce/convert nhmmer output to a bed file?
... @Fatima, great - that should work. Thank you :) ...
written 6 days ago by jamie.pike60
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Is there a way to produce/convert nhmmer output to a bed file?
... I have recently used nhmmer to search for a sequence in a FASTA file, I'd like to compare the output of the nhmmer search to a bed file I have and think it would be easy to do if the nhmmer output is also in bed format. Is there a tool to convert the nhmmer output? I have had a look in the nhmmer ...
nhmmer bed file written 7 days ago by jamie.pike60
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Comment: C: Visualise CD-HIT clusters?
... I was thinking something along the lines of a heatmap that is binary, if that makes sense? The protein clusters are from 9 genomes, 5 from one strain, 4 from another. I was hoping to try and create something that demonstrates a proteins presence in one strain and absence in another. I wasn't sure if ...
written 10 weeks ago by jamie.pike60
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Visualise CD-HIT clusters?
... I have recently clustered a set of proteins using CD-HIT and I was wondering if anyone could recommend a nice way to visualise the clusters (there are 61 clusters in total)? Example of clusters from CD-HIT: >Cluster 0 0 574aa, >GCA_000350365.1_Foc4_1.0_B2_genomic.fna_Candidate_Sequen ...
data visualisation clustering cd-hit written 10 weeks ago by jamie.pike60 • updated 16 days ago by Biostar ♦♦ 20
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Comment: C: *** buffer overflow detected ***: blastclust terminated?? Is there another way t
... Works perfectly, thank you ...
written 10 weeks ago by jamie.pike60
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*** buffer overflow detected ***: blastclust terminated?? Is there another way to create a non-redundant set of proteins?
... I am trying to create a non-redundant set of proteins using blastclust, but I keep getting a buffer overflow error. Is anyone aware of a way to stop this, or can perhaps recommend an alternative program for creating non-redundant protein sets? There are currently 54 proteins in the FASTA. blastclu ...
sequence protein blastclust non-redundant set written 10 weeks ago by jamie.pike60
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Comment: C: Python: regular expression searching error
... Thank you for clarifying. I have now removed the Bio.seq module from my code posted earlier, and it still works. I'm not sure what "fixed" it, but it appears I was way off! I shall certainly heed your advice and will try to familiarise my self with more of BioPythons modules. Thank you for all your ...
written 10 weeks ago by jamie.pike60

Latest awards to jamie.pike

Supporter 10 weeks ago, voted at least 25 times.
Scholar 4 months ago, created an answer that has been accepted. For A: Bedtools intersect not reporting all overlaps

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