Question: Merge Paired-End Reads
8
gravatar for NicoBxl
3.6 years ago by
NicoBxl3.3k
Belgium
NicoBxl3.3k wrote:

Hi,

How can I merge two paired end fastq (R and L) to give a single fastq file ? For information, the sequencing run is 72 bp long and it contains a majority of small RNA (miRNA,...) so a lot of paired end reads will overlap.

For example here's two paired reads :

@HWUSI-EAS529:41:FC62YHFAAXX:8:1:7969:1330 1:N:0:GCCAAT
CTACGAAAGGGCACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCT
+
IIIIIIIHIIHIIIIIIHHIIIHGIIIIEIIIIIIEIIHIIIIIIIIIIIHIIIIIBHIHIIHGIGIEGHHEGEEH


@HWUSI-EAS529:41:FC62YHFAAXX:8:1:7969:1330 2:N:0:GCCAAT
AGTGCCCTTTCGTAGGATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA
+
IIIIIIIIIIIIIIIIIIIIIIIDHIGIIIHIIIGHGIIIIIIIHHIHIIIIIIIIIHIIIIIIIIHIIGIIIIHI

I find the adapter in the first one :

Code:

EMBOSS_001         1 CTACGAAAGGGCACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGC     50
                                    |||||||||||||||||||||              
EMBOSS_001         1 ---------------TGGAATTCTCGGGTGCCAAGG--------------     21

EMBOSS_001        51 CAATATCTCGTATGCCGTCTTCTGCT     76

EMBOSS_001        22 --------------------------     21

but not in the second one ...

But I effectively found the overlap between the right read and the left read (using the reverse complement of it)

EMBOSS_001         1 --------------------------------------------------      0

EMBOSS_001         1 TTTTTTAATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACA     50

EMBOSS_001         1 -----------CTACGAAAGGGCACTTGGAATTCTCGGGTGCCAAGGAAC     39
                                |||||||||||||||                        
EMBOSS_001        51 GTCCGACGATCCTACGAAAGGGCACT------------------------     76

EMBOSS_001        40 TCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCT     76

EMBOSS_001        77 -------------------------------------     76

So my question is, how can I merge the two fastq files to produce a single fastq file ?

Thanks,

N.

ADD COMMENTlink modified 12 weeks ago by Gabriel R.1.4k • written 3.6 years ago by NicoBxl3.3k
2
gravatar for pmenzel
3.6 years ago by
pmenzel310
pmenzel310 wrote:

Maybe this program is suited for you: http://www.cbcb.umd.edu/software/flash/

ADD COMMENTlink written 3.6 years ago by pmenzel310

It's no available, the web page cannot be open. http://genomics.jhu.edu/software/FLASH/index.shtml

ADD REPLYlink written 2.5 years ago by litiancheng.gansu10

It's here now: http://ccb.jhu.edu/software/FLASH/

ADD REPLYlink written 23 months ago by matted4.9k
1
gravatar for Jeremy Leipzig
3.6 years ago by
Philadelphia, PA
Jeremy Leipzig14k wrote:

There is a decent program called stitch:[?] https://github.com/audy/stitch

I wrote a script called mergePairs that is very sensitive and incredibly slow:[?] http://code.google.com/p/standardized-velvet-assembly-report/source/browse/trunk/mergePairs.py

ADD COMMENTlink written 3.6 years ago by Jeremy Leipzig14k
1
gravatar for lelle
23 months ago by
lelle570
Berlin
lelle570 wrote:

As this was referenced from a duplicate question, I will add a newer tool to the list: PANDAseq

ADD COMMENTlink written 23 months ago by lelle570
1
gravatar for Andreas
12 weeks ago by
Andreas2.2k
Singapore
Andreas2.2k wrote:

One more: SeqPrep

Andreas

ADD COMMENTlink written 12 weeks ago by Andreas2.2k
0
gravatar for Stevelor
3.6 years ago by
Stevelor300
Stevelor300 wrote:

Either use Galaxy or use the single scripts

http://hg.notalon.org/galaxy/galaxy-central/src/7d9bb95caaa7/tools/fastq

HTH!

ADD COMMENTlink written 3.6 years ago by Stevelor300
1

uhhh which script?

ADD REPLYlink written 3.6 years ago by Jeremy Leipzig14k
0
gravatar for Gabriel R.
12 weeks ago by
Gabriel R.1.4k
Germany
Gabriel R.1.4k wrote:

If you wish to trim adapters and merge in a single step, you can the leeHom, we use it mainly to reconstruct ancient DNA sequences but it has broader uses as well:

http://nar.oxfordjournals.org/content/42/18/e141

It use a Bayesian maximum a posteriori approach that considers quality scores for both the adapter determination and the merging part. 

ADD COMMENTlink written 12 weeks ago by Gabriel R.1.4k
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