User: Empyrean

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Empyrean150
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Posts by Empyrean

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Comment: C: Extract Base Based On Position From Bam File
... Its not very simple as it looks like. Using this command, i will get the bases on the reads just by giving that position, but i want it according to reference. please read my comments under my post above. that might give you better idea of what i am looking for and help me if you figure out a way to ...
written 4.5 years ago by Empyrean150
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Comment: C: Extract Base Based On Position From Bam File
... thank you johan, also can i give multiple locations? like instead of chr1:1-3, i wanted the bases for following positions on chr:1 - 1, 10, 15 , 20 , 25 , 30. how can i get this information? ...
written 4.5 years ago by Empyrean150
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Haplotype Calling
... Hi I have 454 Amplicon sequencing data for a tetraploid potato crop. we have sequenced few genes of interest from several different genotypes. My aim is to seperate genotypes and sub genomes here. I am thinking of using haplotype analysis to seperate the genotypes as well as sub genomes here. As ...
haplotype calling 454 sequencing written 4.5 years ago by Empyrean150 • updated 2.3 years ago by Biostar ♦♦ 10
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Answer: A: Haplotype Calls From Amplicon Sequencing
... Any help on this issue.. i am struck here ...
written 4.5 years ago by Empyrean150
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Comment: C: Extract Base Based On Position From Bam File
... Thank you for your reply. But i am not looking to get for a interval. you can read my comment from above.. where i am not just looking for bases from read. I am looking for bases after mapping to reference i.e it has to take gaps in to consideration and get as output.. I have some specific snp posit ...
written 4.5 years ago by Empyrean150
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Comment: C: Extract Base Based On Position From Bam File
... ok sure.. I am working on a polyploid organism which has two genomes in it. goal is to seperate them by identifying the markers. So when i identify the snps between them i could not find good heterozygous snps between them. So i wanted to get a haplotype for the read. for that, i use the snps inform ...
written 4.7 years ago by Empyrean150
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Comment: C: Extract Base Based On Position From Bam File
... thank you chris, your solution is perfect for what i have asked but when i saw the output, i realized that the position i need is not with respect to read, but it is based on reference. i have commented to Arun above in a bit detail.. can you suggest any solution for this? ...
written 4.7 years ago by Empyrean150
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Comment: C: Extract Base Based On Position From Bam File
... thank you but this not what i need. I guess i should have made my question clear..sorry about that.. So once the read maps to the reference, i wanted to give input a position based on the reference say 100th position on reference, i need all bases from the reads which are mapping at that particular ...
written 4.7 years ago by Empyrean150
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Comment: C: Extract Base Based On Position From Bam File
... thank you for the answer. But this doesnt help. because when i give this command as input, it again prints the bam file at that positions but not the bases. For example, i have few positions where i got the SNPS, lets say 5, 10 ,15 20 and not all reads will have this variation right !! so for read ...
written 4.7 years ago by Empyrean150
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Extract Base Based On Position From Bam File
... I have a bam file and i wanted to extract the following information. For a read in a bamfile, can i extract the base based on the position? For example, if i say i need the base at 100th position and it should output whether its A/T/G/C. Can i get this using samtools or bamtools?? ...
samtools mpileup written 4.7 years ago by Empyrean150 • updated 4 months ago by stephanieP0

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