The strandness of Trans-ABySS

[Dapeng Wang]

Hi there,

I am using Trans-ABySS to assemble some transcriptoms with RNA-Seq but I am not sure how to set up the strandness arguments for the program.

I know Trinity has four types of definitions for strandness such as RF, FR (for paired-end reads) and F, R (for single-end reads) as follows (from the manual of Trinity website)

• Paired reads:

  • RF: first read (/1) of fragment pair is sequenced as anti-sense (reverse(R)), and second read (/2) is in the sense strand (forward(F)); typical of the dUTP/UDG sequencing method.
  • FR: first read (/1) of fragment pair is sequenced as sense (forward), and second read (/2) is in the antisense strand (reverse)

• Unpaired (single) reads:

• F: the single read is in the sense (forward) orientation
• R: the single read is in the antisense (reverse) orientation

I am wondering how to find the corresponding ways to analyze the 4 types of reads with Trans-ABySS?

Many thanks,

Regards,

Tom

[Ka Ming Nip]

Hi Tom,

Trans-ABySS should be able to handle RF with the `--SS` option.
For FR, you must modify the read files by replacing '/1' with '/2' and vice versa.

For single-end reads, it expects all reads in the forward orientation only. If the reads were in the reverse orientation, they would have to reverse-complemented manually.

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Dapeng Wang [wang...@gmail.com]
Sent: April 29, 2017 2:45 PM
To: Trans-ABySS
Subject: The strandness of Trans-ABySS

Hi there,

I am using Trans-ABySS to assemble some transcriptoms with RNA-Seq but I am not sure how to set up the strandness arguments for the program.

I know Trinity has four types of definitions for strandness such as RF, FR (for paired-end reads) and F, R (for single-end reads) as follows (from the manual of Trinity website)

* Paired reads:

* RF: first read (/1) of fragment pair is sequenced as anti-sense (reverse(R)), and second read (/2) is in the sense strand (forward(F)); typical of the dUTP/UDG sequencing method.
* FR: first read (/1) of fragment pair is sequenced as sense (forward), and second read (/2) is in the antisense strand (reverse)
* Unpaired (single) reads:

* F: the single read is in the sense (forward) orientation
* R: the single read is in the antisense (reverse) orientation

I am wondering how to find the corresponding ways to analyze the 4 types of reads with Trans-ABySS?

Many thanks,

Regards,

Tom

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[Dapeng Wang]

Hi,

I just got some fastq files from SRA database and they seem to have no /1 and /2 but .1 and .2.

Are these notations working for Trans-ABySS to identify the left (.1) and right (.2) ends of the reads in terms of the strandness? If not, which position should /1 and /2 put on in the read header?

----------------------------------------------------------------------------------------------------------------------------

@SRR000001.1.1 TTT-AB356:66:C0YNMMMRR:5:3305:2266:2132 length=100

@SRR000001.1.2 TTT-AB356:66:C0YNMMMRR:5:3305:2266:2132 length=100

----------------------------------------------------------------------------------------------------------------------------

Thank you,

Tom

Ka Ming Nip於 2017年5月1日星期一 UTC+1下午5時25分21秒寫道：

[Ka Ming Nip]

Hi Tom,

You should blat a few of your reads to confirm that '.2' reads are sense to the transcript and the '.1' reads are anti-sense to the transcript.
https://github.com/bcgsc/transabyss/wiki#17-strand-specific-assembly

If so, you can replace '.1' with '/1' and '.2' with '/2'

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Dapeng Wang [wang...@gmail.com]

Sent: May 2, 2017 7:17 AM
To: Trans-ABySS
Subject: Re: The strandness of Trans-ABySS

Hi,

I just got some fastq files from SRA database and they seem to have no /1 and /2 but .1 and .2.

Are these notations working for Trans-ABySS to identify the left (.1) and right (.2) ends of the reads in terms of the strandness? If not, which position should /1 and /2 put on in the read header?

----------------------------------------------------------------------------------------------------------------------------
@SRR000001.1.1 TTT-AB356:66:C0YNMMMRR:5:3305:2266:2132 length=100

@SRR000001.1.2 TTT-AB356:66:C0YNMMMRR:5:3305:2266:2132 length=100

----------------------------------------------------------------------------------------------------------------------------


Thank you,

Tom

Ka Ming Nip於 2017年5月1日星期一 UTC+1下午5時25分21秒寫道：
Hi Tom,

Trans-ABySS should be able to handle RF with the `--SS` option.
For FR, you must modify the read files by replacing '/1' with '/2' and vice versa.

For single-end reads, it expects all reads in the forward orientation only. If the reads were in the reverse orientation, they would have to reverse-complemented manually.

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

From: trans...@googlegroups.com<javascript:> [trans...@googlegroups.com<javascript:>] On Behalf Of Dapeng Wang [wang...@gmail.com<javascript:>]

Sent: April 29, 2017 2:45 PM
To: Trans-ABySS
Subject: The strandness of Trans-ABySS

Hi there,

I am using Trans-ABySS to assemble some transcriptoms with RNA-Seq but I am not sure how to set up the strandness arguments for the program.

I know Trinity has four types of definitions for strandness such as RF, FR (for paired-end reads) and F, R (for single-end reads) as follows (from the manual of Trinity website)


* Paired reads:

* RF: first read (/1) of fragment pair is sequenced as anti-sense (reverse(R)), and second read (/2) is in the sense strand (forward(F)); typical of the dUTP/UDG sequencing method.
* FR: first read (/1) of fragment pair is sequenced as sense (forward), and second read (/2) is in the antisense strand (reverse)
* Unpaired (single) reads:

* F: the single read is in the sense (forward) orientation
* R: the single read is in the antisense (reverse) orientation

I am wondering how to find the corresponding ways to analyze the 4 types of reads with Trans-ABySS?

Many thanks,

Regards,

Tom



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