Barcodes on reverse complement

[msma...@gmail.com]

Hi Lu,

I have been matching the barcodes extracted by bartender to the original reads they came from, and it looks like some reported barcodes are not in the reads themselves, but in their reverse complement.  Is that the intended behavior?  I thought the reads would always be sequenced on the same strand, in which case this shouldn't be necessary, but I may be mistaken.

Many thanks,
Michael

[赵路]

Hi Michael,

Thanks for you email. You are right. For single end reads, bartender should consider only one direction. Initially we provisioned this extractor for both single and pair end reads. I will add an option to bartender so that user can choose whether to consider reverse direction.

Will keep you posted on this and thank you for finding this problem.

Best,

Lu

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Sincerely,

 

Lu

[赵路]

Hi Michael,

Bartender was updated now. I added an option about the strand direction. User can specify the strand direction in bartender extractor. Please let me know if it works to you.

Thank you.

Best,

Lu

--

Sincerely,

 

Lu

[msma...@gmail.com]

Thanks, that works!

Michael

On Saturday, July 29, 2017 at 4:36:47 AM UTC-4, 赵路 wrote:

Hi Michael,

Bartender was updated now. I added an option about the strand direction. User can specify the strand direction in bartender extractor. Please let me know if it works to you.

Thank you.

Best,

Lu

On Fri, Jul 28, 2017 at 9:26 AM, 赵路 <luzha...@gmail.com> wrote:

Hi Michael,

Thanks for you email. You are right. For single end reads, bartender should consider only one direction. Initially we provisioned this extractor for both single and pair end reads. I will add an option to bartender so that user can choose whether to consider reverse direction.

Will keep you posted on this and thank you for finding this problem.

Best,

Lu

On Thu, Jul 27, 2017 at 2:29 AM, <msma...@gmail.com> wrote:

Hi Lu,

I have been matching the barcodes extracted by bartender to the original reads they came from, and it looks like some reported barcodes are not in the reads themselves, but in their reverse complement.  Is that the intended behavior?  I thought the reads would always be sequenced on the same strand, in which case this shouldn't be necessary, but I may be mistaken.

Many thanks,
Michael

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For more options, visit https://groups.google.com/d/optout.

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Sincerely,

 

Lu

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Sincerely,

 

Lu