User: rob234king

gravatar for rob234king
rob234king550
Reputation:
550
Status:
Trusted
Location:
UK/Harpenden/Rothamsted Research
Website:
http://elvis.misc.cran...
Last seen:
3 days, 17 hours ago
Joined:
5 years, 1 month ago
Email:
r*********@gmail.com

Cranfield University MSc Applied Bioinformatics, Queen Mary University of London PhD Cancer Radiopharmaceuticals. Employed at Rothamsted Research.

Posts by rob234king

<prev • 151 results • page 1 of 16 • next >
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falcon unzip output
... I have had errors getting falcon unzip to work on a pacbio assembly but believe I have got to an end by launching jobs manually. I had to change one of the scripts as -mum for nucmer was an option when should have been --mum and was causing an error (I did post on github about this). What I think ...
falcon pacbio written 5 days ago by rob234king550
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Comment: C: falcon-unzip installation and testing using pacbio data
... I got the test data to run using the config file provided in tutorial. It looks like was successful. The raw data was fasta. I just tested with fastq data and ends with error. From ENA they quite often provide the data in fastq so using this tools looks like I can convert https://github.com/zyndagj ...
written 12 weeks ago by rob234king550
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Comment: C: falcon-unzip installation and testing using pacbio data
... I will try this and see if can get it to complete. Thanks ...
written 12 weeks ago by rob234king550
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falcon-unzip installation and testing using pacbio data
... I have installed falcon-unzip as below using the pre-compiled binaries and seems fine cd /home/data/bioinf_resources/programming_tools/ #use virtualenv-2.7 unset PYTHONPATH source falcontest/bin/activate tar xvzf falcon-2017.11.02-16.04-py2.7-ucs4.tar.gz -C falcontest export ...
falcon pacbio written 12 weeks ago by rob234king550
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Comment: C: multi-sample vcf file filtering
... I've tried it and seems to work, shouldn't it be as below for one read or more coverage and 24 or more samples? java -jar dist/vcffilterjdk.jar -F BADDDDD -e 'return variant.getGenotypes().stream().filter(G->G.hasDP() && G.getDP()>0).count()>23;' input.vcf ...
written 10 months ago by rob234king550
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multi-sample vcf file filtering
... I'm looking for a way using a 28 sample merged vcf file to add a filter to the "FILTER" column, so I can remove later any SNP which does not have coverage of at least 1 read across 24 of the 28 samples I have in my one vcf file. Anybody know of a way to do this? I think I have found a post about ho ...
vcf snpsift written 10 months ago by rob234king550 • updated 10 months ago by Pierre Lindenbaum107k
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Total RNA-seq miRNA detection query
... I have **total** RNA-seq sequencing (ribosomal RNA depleted) of single end 49bp stranded RNA from mouse. From total RNA there is these subclasses: mRNA, polyA RNA, polysomal RNA, tRNA, *ribosomal RNA* (removed), lincRNA, miRNA, piRNA, siRNA, SRP RNA, tmRNA, snRNA, snoRNA, SmY RNA, scaRNA, gRNA, aRNA ...
rna-seq written 10 months ago by rob234king550 • updated 10 months ago by mark.ziemann1.0k
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Comment: C: interproscan summary script
... I use blast2go, we have pro licence and function in it to export as spreadsheet interpro domains then use linux command line to count them ...
written 16 months ago by rob234king550
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How to normalise a HTSEQ combined replicate count table
... I have a htseq raw counts table of different tissues rna-seq counts against a custom set of sequences 300 genes. What I would like to do is normalise the counts for each tissue combining the replicates too. I have 2-4 replicates for different tissues with columns G1, G2, G3 etc for each sample follo ...
htseq deseq2 written 23 months ago by rob234king550 • updated 23 months ago by Devon Ryan79k
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search for class of proteins in unannotated genome
... I would like to search an unannotated genome for all amino acid transporters (pfam:PF01490). Whats the most effective way of doing this, blast sounds easy but the proteins are multi exon, I was thinking using hmm's but not sure how and if best option given searching genome. Can anyone recommend and ...
blast written 2.1 years ago by rob234king550 • updated 2.1 years ago by Asaf4.8k

Latest awards to rob234king

Popular Question 6 weeks ago, created a question with more than 1,000 views. For start codon gff annotation corrections using fasta file
Great Question 9 months ago, created a question with more than 5,000 views. For Indel Discovery Delly, Pindel, Samtools, Gatk
Popular Question 9 months ago, created a question with more than 1,000 views. For How to produce a hom/het snp frequency table
Popular Question 9 months ago, created a question with more than 1,000 views. For scripting problem to change string match of one file to another
Popular Question 9 months ago, created a question with more than 1,000 views. For Linux command line use to rename a gff annotation file "Name" attribute
Popular Question 9 months ago, created a question with more than 1,000 views. For Genemark-Es Gtf Output Conversion To Mod
Appreciated 15 months ago, created a post with more than 5 votes. For A: How To Remove Common Variants Present In Two Vcf Files?
Popular Question 15 months ago, created a question with more than 1,000 views. For Linux command line use to rename a gff annotation file "Name" attribute
Popular Question 15 months ago, created a question with more than 1,000 views. For Genemark-Es Gtf Output Conversion To Mod
Popular Question 15 months ago, created a question with more than 1,000 views. For Varscan.V2.3.6 False Positive Snps Being Called
Popular Question 15 months ago, created a question with more than 1,000 views. For scripting problem to use ProtComp output to identify secretome proteins
Great Question 21 months ago, created a question with more than 5,000 views. For New Free Community Tutorial Website For Bioinformatics Learning
Popular Question 21 months ago, created a question with more than 1,000 views. For Merging Multiple De Novo Assembly Fasta Files
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: How To Remove Common Variants Present In Two Vcf Files?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Merging Multiple De Novo Assembly Fasta Files

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