Hi All,
I am quite new in this forum and newbie bioinformatician. I have a very basic question to ask. I have illumina paired-end genomic data with read length 250 bp. I tried some alignment tools to align and map the reads with the reference genome.
At first I used Novoalign. But I found out that it supports maximum read length 150 bp. Though I posted this problem to Novoalign's forum and they advised me that -n 250 would work. It didn't work actually.
Then I was exploring BWA. However, BWA only supports maximum read length 200 bp. On the other hand BWA-SW supports more read length, which I think maximum 1000 kbp or something. But BWA-SW doesn't support pairea-end data.
Then I tried Stampy and it seems taking ages to align and map the data. It took 30 hours and eventually got killed by the system. I think it would not be a wise idea to use a too that takes more than 30 hours to align and map.
I am now at my wits end. Can anyone please tell me, which aligner I can use to align and map paired-end data with read length 250 bp?
Many thanks in advance.
Opulcy
I am quite new in this forum and newbie bioinformatician. I have a very basic question to ask. I have illumina paired-end genomic data with read length 250 bp. I tried some alignment tools to align and map the reads with the reference genome.
At first I used Novoalign. But I found out that it supports maximum read length 150 bp. Though I posted this problem to Novoalign's forum and they advised me that -n 250 would work. It didn't work actually.
Then I was exploring BWA. However, BWA only supports maximum read length 200 bp. On the other hand BWA-SW supports more read length, which I think maximum 1000 kbp or something. But BWA-SW doesn't support pairea-end data.
Then I tried Stampy and it seems taking ages to align and map the data. It took 30 hours and eventually got killed by the system. I think it would not be a wise idea to use a too that takes more than 30 hours to align and map.
I am now at my wits end. Can anyone please tell me, which aligner I can use to align and map paired-end data with read length 250 bp?
Many thanks in advance.
Opulcy
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