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Forum: Bioinformatics 04-22-2015, 01:56 PM
Replies: 0
Views: 1,771
Posted By sandesh
Trinity genome guided error

Hello,
Getting this error after running for many hrs:
Please anybody got into same problem?

#############################################################################
This was the command:
...
Forum: Bioinformatics 03-11-2015, 11:45 AM
Replies: 2
Views: 1,938
Posted By sandesh
It is like this: L 1 2 3 S1 AA GC...

It is like this:
L 1 2 3
S1 AA GC TT
S2 TT CC CC
S3 AT GC TC

How can we make multi fasta from this one?
Forum: Bioinformatics 03-11-2015, 11:02 AM
Replies: 2
Views: 1,938
Posted By sandesh
Construct phylogenetic tree from SNP data?

Hello,

I need to construct phylogenetic tree using SNP data.
Lets say, 100 samples with 50 SNPs.
Is there any software?
or any way that I can try.

Thanks for all suggestions
Sandesh
Forum: Bioinformatics 03-11-2015, 06:58 AM
Replies: 5
Views: 6,198
Posted By sandesh
Thanks I tried vcf-merge

Thanks I tried vcf-merge
Forum: Bioinformatics 03-11-2015, 06:55 AM
Replies: 2
Views: 1,451
Posted By sandesh
Thanks It works

Thanks It works
Forum: Bioinformatics 03-10-2015, 11:49 AM
Replies: 2
Views: 1,451
Posted By sandesh
Bowtie2: direct stderr to a file

Hello All,

How can I direct bowtie2 alignment report (stderr) to a file instead of console?

Thanks
Sandesh
Forum: Bioinformatics 03-06-2015, 06:43 AM
Replies: 5
Views: 6,198
Posted By sandesh
convert vcf to hapmap

I was trying to use SNPhylo software.
I needed to combine multiple SNP vcf files together or use combined hapmap file.
Is there any way to get single vcf or hapmap file with multiple samples...
Forum: Bioinformatics 01-31-2015, 07:37 PM
Replies: 2
Views: 2,581
Posted By sandesh
parallel blat (pblat) error

Hello all,

I found modified blat for parallel running, which has -threads option.
But getting error:

blat Pcap_genome.2bit test-protein.fasta -t=dnax -q=prot -mask=lower test_blat -out=blast8...
Forum: Bioinformatics 01-27-2015, 06:47 AM
Replies: 5
Views: 3,048
Posted By sandesh
Thanks I tried that too. I made 100 parts....

Thanks
I tried that too. I made 100 parts. Running single file took more then 3 days and stopped, which means more then 300 days to go.
Forum: Bioinformatics 01-26-2015, 06:53 AM
Replies: 6
Views: 2,302
Posted By sandesh
Actually I am trying to annotate genome size of...

Actually I am trying to annotate genome size of 65 MB. It has 18 linkage groups with other remaining scaffolds (which may be around 800 small scaffolds). Most of the sequence are in LGs.

I got the...
Forum: Bioinformatics 01-25-2015, 02:10 PM
Replies: 6
Views: 2,302
Posted By sandesh
Thanks for response. I am trying to align...

Thanks for response. I am trying to align uniref90 proteins to get all protein hits and run exonerate later with that hit because running exonerate with uniref90 is really slow. So, i want to filter...
Forum: Bioinformatics 01-25-2015, 01:20 PM
Replies: 7
Views: 5,129
Posted By sandesh
Hello, How can we change AAT protein...

Hello,

How can we change AAT protein alignment output to gff file to be used for EVM.

Thanks Sandesh
Forum: Bioinformatics 01-25-2015, 09:44 AM
Replies: 6
Views: 2,302
Posted By sandesh
Blast multifasta protein to genome and get protein which match to genome.

Hello,

I want to blast multifasta protein to genome and get multifasta protein file with all proteins that aligned to the genome. Is there any way to do this?

It is even fine if I can get all...
Forum: Bioinformatics 01-25-2015, 09:38 AM
Replies: 5
Views: 3,048
Posted By sandesh
I tried exonerate-server too. This one is also...

I tried exonerate-server too. This one is also slow.
Forum: Bioinformatics 01-23-2015, 08:42 PM
Replies: 5
Views: 3,048
Posted By sandesh
exonerate - how to use multiple cores?

Hello,
I used this command to run exonerate:

exonerate -m p2g -q uniref90_modified.fasta -t all_LGs/PcapLG_18.fasta --softmasktarget yes --showvulgar no --showalignment no --showtargetgff yes...
Forum: Bioinformatics 01-23-2015, 01:00 PM
Replies: 2
Views: 1,654
Posted By sandesh
I used command below. uniref90 has got more then...

I used command below. uniref90 has got more then 22 M proteins.
I am not sure if the CPU are used properly.
I have been trying different ways like just running single scaffolds but run forever.
I...
Forum: Bioinformatics 01-23-2015, 10:44 AM
Replies: 2
Views: 1,654
Posted By sandesh
Exonerate uniref90.fasta alignment to 65MB genome

Hello,

I was trying to align uniref90.fasta (10 gb) to genome for annotation.
I have 64 GB ram with 32 core.
It is already running since a month.:confused:
I was wondering if it is normal or...
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