It depends whether the read maps to one or multiple locations - if the aligner can determine the position of one read in a pair uniquely, but can't map the other one, I don't see why there would be a problem in using the one that mapped, especially since the reads are pretty long nowdays (>70bp).
Cufflinks Paired End Read Names
Could you please tell me the proper way in which the read names need to be formatted in a bam file containing paired end reads, for the cufflinks to recognize them as paired end reads and not single reads? Do they need to have a proper suffix (e.g. _1/_2) or the names need to be the same?
On a similar note, can cufflinks handle bam files with mixed single and paired reads?
Tnx!
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We don't need any suffix in the bam file for reads that belong to a pair. You can use flags to determine which reads is first in pair and which is second in pair.
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Frenkiboy: While dealing with Paired read, How you tackle the issue when one part of the pair is not mappable due to some reasons ? Wouldn't it give some odd results in such cases ?
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