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Forum: De novo discovery 08-18-2011, 01:57 AM
Replies: 16
Views: 13,477
Posted By mghita
Does anyone know how to allow for SNPs when...

Does anyone know how to allow for SNPs when assembling sequences with Velvet?

I have downloaded Velvet 1.1.05 and obtained some contigs using my reads, but they don't have SNPs and I am quite sure...
Forum: Bioinformatics 08-16-2011, 01:28 AM
Replies: 132
Views: 44,623
Posted By mghita
Initially, that was what I was intended, but I...

Initially, that was what I was intended, but I have discovered that other reads include a series of N's, so now I am interested in removing the reads that have N's inside. cutadapt did not work for...
Forum: Bioinformatics 08-15-2011, 02:44 AM
Replies: 132
Views: 44,623
Posted By mghita
I have a problem using cutadapt. The output file...

I have a problem using cutadapt. The output file still contain the adapter. What am I doing wrong?

cutadapt -a N ~/Desktop/pr/reads1.fq > ~/Desktop/pr/reads.fq


When I use the program, it...
Forum: Bioinformatics 08-15-2011, 02:03 AM
Replies: 132
Views: 44,623
Posted By mghita
Hi, I am trying to use cutadapt to trim the...

Hi, I am trying to use cutadapt to trim the adapter in some illumina reads, the adapter is on the first position. The output still contains the adapter. What am I doing wrong?

cutadapt -a N...
Forum: Bioinformatics 08-10-2011, 07:13 AM
Replies: 10
Views: 14,827
Posted By mghita
Hi, What options should I use in bwa in...

Hi,

What options should I use in bwa in order to obtain perfect maps only? I have two references and I would like to get the unique perfect maps to both of them (in two different files if...
Forum: Bioinformatics 08-09-2011, 05:58 AM
Replies: 26
Views: 40,604
Posted By mghita
I have given up. I replaced the @ with > and...

I have given up. I replaced the @ with > and still didn't work. I have combined a little awk and R and does my job just fine. Thanks a lot for the effort!

Madalina
Forum: Bioinformatics 08-09-2011, 01:28 AM
Replies: 26
Views: 40,604
Posted By mghita
Hi, Yes, that seems to work, but the command...

Hi,

Yes, that seems to work, but the command itself doesn't. The reads in my fasta file (file.fas) are named @Frag_1, @Frag_2 .... @Frag_20000. I want to extract some of them - I have their names...
Forum: Bioinformatics 08-08-2011, 09:46 AM
Replies: 26
Views: 40,604
Posted By mghita
I have Mac OS X 10.6.8, 3.06 GHz. I just get that...

I have Mac OS X 10.6.8, 3.06 GHz. I just get that message in bash, I don't get any install option. I tried to download it, but it doesn't work.
Forum: Bioinformatics 08-08-2011, 09:20 AM
Replies: 26
Views: 40,604
Posted By mghita
I have added the program to my path and I set the...

I have added the program to my path and I set the permission right, but now I have another issue:
"You need the Rosetta software to run faSomeRecords. The Rosetta installer is in Optional Installs...
Forum: Bioinformatics 08-05-2011, 09:43 AM
Replies: 26
Views: 40,604
Posted By mghita
Hi

Hi,

I might sound dumb to people around here :D, but how do I install/open/use the command? I tried faSomeRecords in.fa listFile out.fa with my files and it says "-bash: faSomeRecords: command not...
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