I have a doubt in mapping studies
I had taken a set of proteins and obtained the mRNA from NCBI and then converted them in to reads using a perl program. If i want to map them back to the reference sequence, I used BWA and I want to visualize the mapped file [sam format] using tablet viewer.
1. since I did a fasta to fastq conversion, and if the mRNA coding the hypothetical protein was expressed in the negative strand, will it be meaningful if i wish to map this mRNA [cDNA] to the reference sequence. Or in other words, should i also take the complement of this sequence and then convert it in to fastq format. pls let me know
2. When, I did a mapping of these sequences against the reference sequence, for each mRNA sequence, I got it mapped to 16 different locations in the reference sequence and in fact none of them were overlapping. This is what i understood by looking at the beginning and ending coordinates of each alignment in the SAM file.
3. I wished to view this mapping in a tablet viewer, but it shows an error everytime i load [java.source.lang not found]. Though other java programs runs effectively, I am unable to view the output.
4. If I want to find the promoters of one such protein, i thought of taking 200bp upstream to the beginning of the gene site and then get the corresponding coordinates. But is the prediction approach correct.
pls help
with regards
N. Rathankar
I had taken a set of proteins and obtained the mRNA from NCBI and then converted them in to reads using a perl program. If i want to map them back to the reference sequence, I used BWA and I want to visualize the mapped file [sam format] using tablet viewer.
1. since I did a fasta to fastq conversion, and if the mRNA coding the hypothetical protein was expressed in the negative strand, will it be meaningful if i wish to map this mRNA [cDNA] to the reference sequence. Or in other words, should i also take the complement of this sequence and then convert it in to fastq format. pls let me know
2. When, I did a mapping of these sequences against the reference sequence, for each mRNA sequence, I got it mapped to 16 different locations in the reference sequence and in fact none of them were overlapping. This is what i understood by looking at the beginning and ending coordinates of each alignment in the SAM file.
3. I wished to view this mapping in a tablet viewer, but it shows an error everytime i load [java.source.lang not found]. Though other java programs runs effectively, I am unable to view the output.
4. If I want to find the promoters of one such protein, i thought of taking 200bp upstream to the beginning of the gene site and then get the corresponding coordinates. But is the prediction approach correct.
pls help
with regards
N. Rathankar
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