[miltron]

Thanks Ben!
That was a very quick reply! I will try this
Best,
Miltron

[Ben Langmead]

Hi Miltron,

I would recommend trying --offrate 6 and, if that doesn't work, --offrate 7. Those will use a sparser sample of the suffix array than is included in the index by default, which in turn reduces memory footprint. If that doesn't work, I would suggest running on a computer with more memory. The mouse genome is big

Good luck,
Ben

[miltron]

Hi, I'm a new member and I'm trying to use Bowtie to align some ChIPseq data. First of all, I'm really grateful that you are putting your efforts into this and really keeping an eye on this board it seems.

I installed Bowtie binaries for Windows on my Windows 7 system and I'm trying to use Cygwin to run it. I have 4GB of RAM installed on this computer. According to the documentation I thought that should have been appropriate memory for my purpose, but I might be understanding.

I'm assembling reads from 2.5 GB file to Mouse mm9 assembly and using the pre-built indexes reccommended in the Bowtie manual.

However, when I run bowtie I get the following error message:

Time loading forward index: 00:00:14
Out of memory allocating the ebwt[] array for the Bowtie index. Please try
again on a computer with more memory.
Time loading mirror index: 00:00:01
Time searching: 00:00:15
Overall time: 00:00:15
Command: C:\users\erna\desktop\bowtie-0.12.5-win32\bowtie-0.12.5\bowtie.exe -t -
m 1 -v 2 -q --best mm9 reads/seq3.fastq seq3align.map


I've tried to increase the memory allocated to Cygwin to no avail. Do you think that finding another Windows system with more memory will help?
Thanks!

[Ben Langmead]

I have a question with Bowtie. Does the bowtie-build command create a different index everytime it is run on the same data? Myself and my colleague are creating an index of the Drosophila genome. But he says that the builds are different everytime one runs it. Is this true? If so how is the downstream process (Tophat, Cufflinks) outputs comparable to each other.

Hi gen2prot,

If you run Bowtie twice on the same exact set of fasta files (same sequence names and sequence characters), specified in the same exact order, you should get the same exact index. If you don't, there's something wrong. If you have an example where it doesn't (the smaller the better), please email me.

Thanks,
Ben

[gen2prot]

Hello Ben,

I have a question with Bowtie. Does the bowtie-build command create a different index everytime it is run on the same data? Myself and my colleague are creating an index of the Drosophila genome. But he says that the builds are different everytime one runs it. Is this true? If so how is the downstream process (Tophat, Cufflinks) outputs comparable to each other.

Thanks
Abhijit

[bio_tt]

hi,
bowtie is very popular,but i am a newer.and you say"Includes tool to convert Bowtie output to a Maq .map file ",but i don't know how to write the command line?could you help me? thanks

[seq_GA]

I managed to figure out the problem. I was using -f option for input file instead of -q option for inputfastq format. Thanks.

[seq_GA]

Hi,
I have downloaded fastq file format from ncbi (Illumina reads) and trying to use Bowtie and I get the following error.

Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'

Let me know how to overcome this problem. Thanks.

[guisinmm]

I'm new to NGS, and I'm wondering if Bowtie could be of use to me. I have Illumina reads, and I want to assemble chloroplast genomes. I have built an index using another chloroplast genome, and I am successful in running Bowtie using default parameters. Sequence differences should be relatively minor in coding regions, but they could be significant in non-coding regions. I'll need to tweek the parameters accordingly, I guess. So, here are my questions: Would Bowtie be useful for me? How would you suggest I set -n or -v to allow for between species sequence differences? Once I get the output, how can I map these to the reference to create contigs? I see the location of the alignment in the output, but what step do I take next to work with the output?

Thanks for the help!
guisinmm

[Ben Langmead]

Hi Ben, how different are hg18 and NCBI36 genomes? Genomic co-ordinates for quite a few single nucleotide mutations obtained from RNAseq data based on bowtie hg18 index are not mapping to the same bases on NCBI36.
Thanx,-s

My understanding is that they're hg18 and NCBI v36.* are the same. See, e.g., the first question on this faq:

http://genome.ucsc.edu/FAQ/FAQreleases.html

Thanks,
Ben

[Ben Langmead]

I have a reference genome that is in fact a collection of many contigs whose lengths range between a few hundreds to a few thousands bps. Also most of my reads probably won't align to any of the contigs. Will bowtie work for such case?

Thanks,
Itai

Yes, it should.
Ben

[Subho]

Hi Ben, how different are hg18 and NCBI36 genomes? Genomic co-ordinates for quite a few single nucleotide mutations obtained from RNAseq data based on bowtie hg18 index are not mapping to the same bases on NCBI36.
Thanx,-s

[isharon]

I have a reference genome that is in fact a collection of many contigs whose lengths range between a few hundreds to a few thousands bps. Also most of my reads probably won't align to any of the contigs. Will bowtie work for such case?

Thanks,
Itai

[Lien]

Hi again,

I performed a paired-end run on the Illumina, with 100bp reads. The original DNA fragments are +/- 200 bp. I have a percentage of about 40% of the reads that failed to align. I think some of the original DNA fragments are smaller than 200 bp, so there would be an overlap between both paired reads. To solve this, I think I would have to change the minimum insert size. But this would mean that this number would become negative (for example -30). Is this possible?

Thanks!

[Lien]

Hello,

I have the same problems using a 64-bit computer ('Warning: Exhausted best-first chunk memory for read HWUSI_ ...; skipping read). My paired-end data are in .txt format. Could this have anything to do with the problem? Otherwise, as I'm only starting to work with these data, I have no clue to other things that could be causing this problem.

Thanks a lot!
Lien

Apparently, it is normal that some reads are skipped because they can't align. Just hope the percentage that is skipped isn't too high!