We sequenced the mate pair library with both 250bp MiSeq and 101bp illumina reads. But in the manual, the bowtie2 only accepts two reads. Can it support 4 reads?
Thanks
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Bowtie2 does support the use of multiple files for mate pair libraries,
here I copy the chunk of the bowtie2 manual that explains this. I should
emphasize that the metassembler's input parameters "bowtie2_read1" and
"bowtie2_read2" are directly copied to the corresponding bowtie2 parameters
-1 and -2.
-1 <m1>
Comma-separated list of files containing mate 1s (filename usually includes
_1), e.g. -1 flyA_1.fq,flyB_1.fq. Sequences specified with this option must
correspond file-for-file and read-for-read with those specified in <m2>.
Reads may be a mix of different lengths. If - is specified, bowtie2 will
read the mate 1s from the "standard in" or "stdin" filehandle.
-2 <m2>
Comma-separated list of files containing mate 2s (filename usually includes
_2), e.g. -2 flyA_2.fq,flyB_2.fq. Sequences specified with this option must
correspond file-for-file and read-for-read with those specified in <m1>.
Reads may be a mix of different lengths. If - is specified, bowtie2 will
read the mate 2s from the "standard in" or "stdin" filehandle.
We sequenced the mate pair library with both 250bp MiSeq and 101bp
illumina reads. But in the manual, the bowtie2 only accepts two reads. Can
it support 4 reads?
Hola Alejandro,
About this question i also have two mate pair libraries of 5kb and 8kb of insert size for trying metassembly with 6 assemblies, and although you have explained how to manage the fastq pairs in the configuration i wonder about how to deal with the mateAn parameters. I am using mateAn_s and mate_An_m, how i can configure these two parameters for mananing both libaries and also how i can configure the bowtie_2 maxims and minims? Thank you in advance for your reply
crlx
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Our program works with libraries of one insert size at a time, so you'll
need to use either the 5kb or the 8kb library (you can use the other in a
second run of the metassembler though).
If you have good estimates for the mean insert size and the standard
deviation of insert sizes the you should input these in the parameters
mateAn_m and mateAn_s. Otherwise you can set the parameters mateAn_A and
mateAn_B to establish a expected range of insert sizes [A,B], the mean
insert size and standard deviation will then be computed using inserts
whose length fall within this range.
The bowtie2_maxins and bowtie2_minins are directly copied to the
corresponding bowtie2 parameters: --maxins and ---minins respectively;
these set the minimum and maximum insert length permited for paired reads.
Hola Alejandro,
About this question i also have two mate pair libraries of 5kb and 8kb of
insert size for trying metassembly with 6 assemblies, and although you have
explained how to manage the fastq pairs in the configuration i wonder about
how to deal with the mateAn parameters. I am using mateAn_s and mate_An_m,
how i can configure these two parameters for mananing both libaries and
also how i can configure the bowtie_2 maxims and minims? Thank you in
advance for your reply
crlx
When you said: Our program works with libraries of one insert size at a time, so you'll
need to use either the 5kb or the 8kb library (you can use the other in a
second run of the metassembler though).
How do you exactly do the second run?
Suppose you already meta-assembled scaffolds A and B into A-B using 5kb library. How do you proceed with the second run using 8kb library?
I am interested in using metassembler too, and I have 4 mate-pair libraries.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
You would just use the output of the metassembler from the first library
size as the input to the metassembler for the next library size. However, I
would expect very marginal improvements as you moved from one size to the
next
When you said: Our program works with libraries of one insert size at a
time, so you'll
need to use either the 5kb or the 8kb library (you can use the other in a
second run of the metassembler though).
How do you exactly do the second run?
Suppose you already meta-assembled scaffolds A and B into A-B using 5kb
library. How do you proceed with the second run using 8kb library?
I am interested in using metassembler too, and I have 4 mate-pair
libraries.
No, the point of it is to merge together multiple assemblies into a single
consensus version so you will have to give it multiple fasta files. If you
have multiple libraries you want to use, use the output from the first
library as one extra assembly to be used as input for the next library.
We sequenced the mate pair library with both 250bp MiSeq and 101bp illumina reads. But in the manual, the bowtie2 only accepts two reads. Can it support 4 reads?
Thanks
Hi,
Bowtie2 does support the use of multiple files for mate pair libraries,
here I copy the chunk of the bowtie2 manual that explains this. I should
emphasize that the metassembler's input parameters "bowtie2_read1" and
"bowtie2_read2" are directly copied to the corresponding bowtie2 parameters
-1 and -2.
-1 <m1>
Comma-separated list of files containing mate 1s (filename usually includes
_1), e.g. -1 flyA_1.fq,flyB_1.fq. Sequences specified with this option must
correspond file-for-file and read-for-read with those specified in <m2>.
Reads may be a mix of different lengths. If - is specified, bowtie2 will
read the mate 1s from the "standard in" or "stdin" filehandle.
-2 <m2>
Comma-separated list of files containing mate 2s (filename usually includes
_2), e.g. -2 flyA_2.fq,flyB_2.fq. Sequences specified with this option must
correspond file-for-file and read-for-read with those specified in <m1>.
Reads may be a mix of different lengths. If - is specified, bowtie2 will
read the mate 2s from the "standard in" or "stdin" filehandle.
On Sat, May 28, 2016 at 4:43 PM, Yucheng Zhang yuchengzhang@users.sf.net
wrote:
Hola Alejandro,
About this question i also have two mate pair libraries of 5kb and 8kb of insert size for trying metassembly with 6 assemblies, and although you have explained how to manage the fastq pairs in the configuration i wonder about how to deal with the mateAn parameters. I am using mateAn_s and mate_An_m, how i can configure these two parameters for mananing both libaries and also how i can configure the bowtie_2 maxims and minims? Thank you in advance for your reply
crlx
Hi,
Our program works with libraries of one insert size at a time, so you'll
need to use either the 5kb or the 8kb library (you can use the other in a
second run of the metassembler though).
If you have good estimates for the mean insert size and the standard
deviation of insert sizes the you should input these in the parameters
mateAn_m and mateAn_s. Otherwise you can set the parameters mateAn_A and
mateAn_B to establish a expected range of insert sizes [A,B], the mean
insert size and standard deviation will then be computed using inserts
whose length fall within this range.
The bowtie2_maxins and bowtie2_minins are directly copied to the
corresponding bowtie2 parameters: --maxins and ---minins respectively;
these set the minimum and maximum insert length permited for paired reads.
Wences
On Wed, Jun 22, 2016 at 10:32 AM, Carlos Llorens cllorens@users.sf.net
wrote:
When you said: Our program works with libraries of one insert size at a time, so you'll
need to use either the 5kb or the 8kb library (you can use the other in a
second run of the metassembler though).
How do you exactly do the second run?
Suppose you already meta-assembled scaffolds A and B into A-B using 5kb library. How do you proceed with the second run using 8kb library?
I am interested in using metassembler too, and I have 4 mate-pair libraries.
You would just use the output of the metassembler from the first library
size as the input to the metassembler for the next library size. However, I
would expect very marginal improvements as you moved from one size to the
next
Good luck
Mike
On Tue, Dec 20, 2016 at 1:15 AM, Habib R habibr@users.sf.net wrote:
So, you just give metassembler one input fasta, right?
No, the point of it is to merge together multiple assemblies into a single
consensus version so you will have to give it multiple fasta files. If you
have multiple libraries you want to use, use the output from the first
library as one extra assembly to be used as input for the next library.
Hope this helps,
Mike
On Tue, Dec 20, 2016 at 11:22 PM, Habib R habibr@users.sf.net wrote:
Ok thank you i´ll d so.
crlx