User: ab.tsubaki

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ab.tsubaki50
Reputation:
50
Status:
New User
Location:
South Africa
Last seen:
1 year, 4 months ago
Joined:
4 years, 9 months ago
Email:
a*********@gmail.com

Posts by ab.tsubaki

<prev • 22 results • page 1 of 3 • next >
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Interpreting bed file...
... Hi there I hope someone can help me out here. I have a bed file that I obtained from a bamfile and I am struggling to interpret what the columns mean. The pipeline I followed was as follows: From my gff file I used getfastabed and the output was aligned using bowtie to paired end fastq files. The s ...
bedfile gff bamfile written 2.9 years ago by ab.tsubaki50 • updated 2.9 years ago by michael.ante3.0k
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SyMap database error
... Hi guys   Anyone out there with some experience using SyMap and MySQL? I am working on Linux, Symap installed successfully and MySQL as well. MySQL is running successfully: $ sudo /etc/init.d/mysql status  * /usr/bin/mysqladmin  Ver 8.42 Distrib 5.5.46, for debian-linux-gnu on x86_64 Copyright ( ...
symap mysql written 3.3 years ago by ab.tsubaki50
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Biopython's GenomeDiagram input files???
... Hi all   I am currently trying to draw up a synteny map using Biopython's GenomeDiagram package. I have been able to complete some examples with .gb files and now I want to try it on my own data. Problem: my data is in fasta format???? Any one with experience on this? 1) Can GenomeDiagram use f ...
biopython synteny genomediagram written 3.3 years ago by ab.tsubaki50 • updated 3.3 years ago by mgalactus720
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BLAST Tools: asn2gb????
... Hi guys   Does anyone have any experience in running BLAST Tools asn2gb which converts .asn files to genbank?   I am struggling to get mine running and would love to see an example of a script or any such thing please?!?!   Thanks! ...
file convert blast tools asn2gb written 3.3 years ago by ab.tsubaki50
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Mapping BAM/SAM file back to reference?!?!
... Hi all So I have used BWA to align fastq files (mate pair, Illumina HiSeq) to a reference sequence. I then extracted the unmapped reads using samtools which gives me a bam file.   I would like to take this bam file and map it back to my reference sequence using BWA again. However bam files don't ...
bam reference sam bwa written 3.4 years ago by ab.tsubaki50
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(Closed) MySQL HELP! (For use with SyMap)
... Hi everyone I'm trying to use SyMap to draw up some synteny maps and for I have been trying to get MySQL up and running in order to run larger data sets. From the MySQL website I have started to download, unpack and install MySQL up to the Post installation process. However, I keep running into er ...
mysql written 3.4 years ago by ab.tsubaki50
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Comment: C: Estimating genome size from k-mer histograms...
... Thanks Matt. That IS a very useful site. I've taken a look.  I tried attaching an image but couldn't figure out how. The main problem is that my histogram's shape does not lend itself to genome size estimation at all. You can describe the graph as "monotonically descending, exponential decay kmer h ...
written 4.6 years ago by ab.tsubaki50
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Estimating genome size from k-mer histograms...
... Hi all Anyone with experience using Jellyfish derived histograms? I've done all the necessary bits and now I get to drawing up my histogram and it looks nothing like its supposed to! There's no peak or humps - it just starts at the top and slopes downward to flatten out at the bottom! The scripts ...
kmer next-gen genome size written 4.6 years ago by ab.tsubaki50 • updated 10 months ago by h.mon23k
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Jellyfish error on compiling
... Hi   Any Jellyfish users out there? I've downloaded the program, configured it successfully - but when I type "make" i get the following errors: make  all-am make[1]: Entering directory `/scratch/abierman'   CXX    lib/rectangular_binary_matrix.lo   CXX    lib/mer_dna.lo   CXX    lib/storage.lo ...
next-gen jellyfish written 4.6 years ago by ab.tsubaki50
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Help! I'm trying to use DSK k mer counting software and GCE to estimate genomic characters
... Hi all   Can ANYONE please point me in the right direction for help with DSK and GCE? I have been able to successfully run DSK but I don't know what to do with the binary output files??? I have found some info on GCE (http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/gce/README.txt.htm a ...
next-gen k mer genome size written 4.6 years ago by ab.tsubaki50 • updated 4.6 years ago by Rayan Chikhi1.4k

Latest awards to ab.tsubaki

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Masking repetitive sequences ...can I then map using BWA?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Jellyfish error on compiling
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Sequence alignment help: BWA is not my friend!
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Sequence alignment help: BWA is not my friend!

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