User: rob234king
rob234king • 550
- 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
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... 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 ...
written 5 days ago by
rob234king • 550
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... 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
rob234king • 550
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... I will try this and see if can get it to complete. Thanks
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written 12 weeks ago by
rob234king • 550
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... 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 ...
written 12 weeks ago by
rob234king • 550
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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
rob234king • 550
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... 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 ...
written 10 months ago by
rob234king • 550
• updated
10 months ago by
Pierre Lindenbaum ♦ 107k
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... 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 ...
written 10 months ago by
rob234king • 550
• updated
10 months ago by
mark.ziemann • 1.0k
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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
rob234king • 550
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... 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 ...
written 23 months ago by
rob234king • 550
• updated
23 months ago by
Devon Ryan ♦ 79k
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... 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 ...
written 2.1 years ago by
rob234king • 550
• updated
2.1 years ago by
Asaf ♦ 4.8k
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