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Forum: RNA Sequencing 06-14-2016, 04:11 PM
Replies: 0
Views: 1,782
Posted By Autotroph
FPKM vs gene length

Hi,

I used the program RSEM to calculate the expression level of genes in my RNA-seq data (Illumina paired-end) from human cell lines.

Now i see that the FPKM and gene length are positively...
Forum: Bioinformatics 05-30-2016, 11:18 AM
Replies: 0
Views: 1,437
Posted By Autotroph
Recombination fraction estimation from VCF file

Hi,

Could you please suggest a good tool or script that is able to calculate recombination fraction (for haploid progeny of diploid parent) starting from a vcf file?

I have the phased genotypes...
Forum: Genomic Resequencing 04-30-2013, 08:35 AM
Replies: 0
Views: 1,482
Posted By Autotroph
Talking Scaffold end SNPs and artifact checks

Hi,

I have been reading this blogpost (http://pathogenomics.bham.ac.uk/blog/2013/01/sequencing-data-i-want-the-truth-you-cant-handle-the-truth/) about SNP calling artifacts.

It does not...
Forum: Sample Prep / Library Generation 04-19-2011, 07:39 AM
Replies: 7
Views: 3,556
Posted By Autotroph
thanks... i did manage to get less...

thanks...

i did manage to get less fragmented dna with phenol extraction with the pipette tip cut off..
Forum: Bioinformatics 03-08-2011, 04:59 AM
Replies: 16
Views: 5,881
Posted By Autotroph
Smile Hi boetsie, Thanks a lot for the patient...

Hi boetsie,

Thanks a lot for the patient explanation.
Forum: Bioinformatics 03-08-2011, 04:26 AM
Replies: 16
Views: 5,881
Posted By Autotroph
The point of giving an insert size of 100(50+50)...

The point of giving an insert size of 100(50+50) is to not have any gaps in the final scaffold. I understood that the two reads could even overlap if an insert size less than 100 is given for 2*50 bp...
Forum: Bioinformatics 03-08-2011, 01:10 AM
Replies: 16
Views: 5,881
Posted By Autotroph
unfortunately Minimus can be used to merge...

unfortunately Minimus can be used to merge contigs only, not scaffolds.Bambus is able to merge scaffolds but does not allow N's in the input.

It might be possible for me to use Minimus and SSPACE...
Forum: Bioinformatics 03-07-2011, 08:38 PM
Replies: 16
Views: 5,881
Posted By Autotroph
longer reads

Thanks for the clarification Boetsie,

Bowtie can handle only reads that are a maximum of 1024 BP long. What does SSPACE do for reads that are longer than that?

I am interested in merging...
Forum: Sample Prep / Library Generation 03-01-2011, 06:11 AM
Replies: 7
Views: 3,556
Posted By Autotroph
6kb Mate pair Illumina library

Hi,

Before sending in a sample for 6kb Mate pair library preparation what should be the size range of the DNA?

I have extracted Eukaryotic DNA and run it beside a high range ladder (the highest...
Forum: Bioinformatics 02-21-2011, 01:00 PM
Replies: 0
Views: 2,302
Posted By Autotroph
SOAP denovo output to AFG format

Hi,

Soap denovo gives out scaffold sequences with "N's" in place of gaps.

Is anybody aware of a script or tool to convert it to .afg format?

toAMOS just converts fasta files or mate files....
Forum: Bioinformatics 02-16-2011, 08:51 PM
Replies: 16
Views: 5,881
Posted By Autotroph
Thanks. Ya i guess i will be extending the...

Thanks.

Ya i guess i will be extending the previous scaffolds.

The problem with using SSPACE is that it does not allow N's in the input contig file.

The scaffolds which i have are having...
Forum: Bioinformatics 02-16-2011, 03:51 AM
Replies: 16
Views: 5,881
Posted By Autotroph
Scaffolding problem

Hi,

I have these scaffolds with different sizes(1 to 200 kb) from a previous assembly.

Now there is some new data with 3 and 5kb insert paired end. I want to add these paired end reads onto...
Forum: Bioinformatics 02-14-2011, 02:59 AM
Replies: 2
Views: 9,120
Posted By Autotroph
Thanks Thorondor.

Thanks Thorondor.
Forum: Bioinformatics 02-11-2011, 02:38 AM
Replies: 2
Views: 9,120
Posted By Autotroph
kmer vs accuracy

Hi,

Given below is an explanation that i found for the different kmer size and its effect on sensitivity and specificity.

"A smaller k-mer value allows locating more overlapping
sequence (i.e....
Forum: Metagenomics 11-22-2010, 12:56 AM
Replies: 1
Views: 4,565
Posted By Autotroph
Meta assembly

Hi,

I want to do a meta assembly using contigs generated from 8 different locations for the same organism(same technology-Illumina reads).

How should i proceed? Should i just run an assembly...
Forum: Epigenetics 11-22-2010, 12:51 AM
Replies: 0
Views: 1,447
Posted By Autotroph
Genome wide methylation dataset

Hi,

I am looking for genome wide methylation maps for germ line cells(preferably human).

Could you please direct me to any such publicly available dataset?
Forum: Bioinformatics 10-21-2010, 07:08 AM
Replies: 11
Views: 6,218
Posted By Autotroph
Yes, i mailed him with a suggestion to include...

Yes, i mailed him with a suggestion to include the read number at the end of the accession number. This should give unique accession numbers as long as the input accession numbers are unique :)
Forum: Bioinformatics 10-21-2010, 02:07 AM
Replies: 11
Views: 6,218
Posted By Autotroph
The problem seemed to have many components to it....

The problem seemed to have many components to it.
1)Flowsim produced duplicate accession numbers when cutting at the same base twice.
2)Newbler does not accept duplicate accession numbers
3)The...
Forum: Bioinformatics 10-16-2010, 08:10 AM
Replies: 11
Views: 6,218
Posted By Autotroph
Unfortunately runAssembly failed when i tried...

Unfortunately runAssembly failed when i tried with 1111 sff files,The assembly was going fine for smaller datasets.I dint change the command, just added more files into the data directory.

Have i...
Forum: Bioinformatics 10-13-2010, 11:50 PM
Replies: 11
Views: 6,218
Posted By Autotroph
Thanks flxlex I tried this for about 500...

Thanks flxlex

I tried this for about 500 files and it worked. Hope it works as the incremental procedure continues.

Well, the explanation is 100 000 sff files are not real data. It was...
Forum: Bioinformatics 10-13-2010, 03:34 PM
Replies: 11
Views: 6,218
Posted By Autotroph
sfffile vs addRun

Thanks maubp

sfffile merges the sff files in a given directory. The performance of sfffile and addRun seem to be same. However, addRun is better as it also adds it to the project simultaneously. ...
Forum: Bioinformatics 10-13-2010, 02:23 PM
Replies: 11
Views: 6,218
Posted By Autotroph
running Newbler with a lot off .sff files

I have around 1,00,000 .sff files that i want to use for doing an assembly with Newbler.

What would be the best strategy to use?

1)Combine the .sff files? Please let me know how i would do the...
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