Should or can paired-end fastq be converted to single-end fastq -- and the reverse?

usegalaxy.org support
1

how can i turn a single end data, into the paired end data and opposite( paired end into single end data)
?

1 Like
2

Hi @amir

Data that is paired-end or single-end refers to the way the reads were originally sequenced. Any type of manipulation to attempt to create one from the other, either way, is unlikely to produce meaningful scientific results (eg: combining paired-end reads into some type of “fake” single end read dataset). Or, result in data loss (eg: just using the F or R reads from a paired-end dataset as a single end dataset).

What is your goal? Analysis, tools, etc? Or was this just a general question?

1 Like
3

i have this data :
It is 42bp paired-end sequencing; NextSeq was set for 42 bp for read 1, 6 bp for the multiplexing index, and 42 bp for read 2, so a total of 90 reads, 84 of which are supposed to be RNA. So, they should be 2x42bp reads.

now i can just work with 42 bp reads. and if i cut only 20 bp of it, it became useless. i thought maybe or some how combine the paired to get more nucleotide to work with

admin edit for “nucleotide” to remove problematic google search link

4

Hi, I’m not sure what you mean by this, the link appeared to be a google search?

Anyway – use the data as paired-end inputs. Not only does this preserve the true content, but read pairs are an important scientific content advantage for many analysis protocols.

5

You can not go from single-end to paired-end. Maybe you can think of something to simulate it but this data is not useable for doing an actual analyses. To go from paired-end to single-end (wrong terminology see first reply of jennaj) you could use something like FLASH. If you need to do some mapping, most tools can handle paired-end data.

1 Like
6

Thank you @gbbio for adding in this detail. Agree with everything you state.

For some cases where the reads actually overlap, this type of micro “assembly” to generate a consensus is appropriate. And yes, that would not technically result in “single-end” data and shouldn’t be used that way.

@amir To learn more about FLASH, see the tool form. A short description is in the help section and link to the publication is at the bottom. :slight_smile: