User: annadv77

gravatar for annadv77
annadv7720
Reputation:
20
Status:
New User
Location:
Canada
Last seen:
1 year, 6 months ago
Joined:
3 years, 1 month ago
Email:
a*******@gmail.com

Posts by annadv77

<prev • 12 results • page 1 of 2 • next >
1
vote
0
answers
371
views
0
answers
Analyzing AmpliSeq data with Galaxy
... Dear All, I am going to have to analyze data obtained from AmpliSeq Technology (the full panel containing about 20,000 genes), and I was wondering whether I could use Galaxy for that. I am currently using Galaxy for RNAseq analyses, but as I understand, I won't be able to use exactly the same tool ...
ampliseq galaxy tmap written 18 months ago by annadv7720
0
votes
1
answer
905
views
1
answers
Answer: A: Question: SAM-to-BAM: fatal exit code Error 139
... Dear All, I think that I've found the source of the problem I was having - although I did obtain the SAM file, the alignment was very poor, with very low MAPQ scores (0s), so if I understand correctly, that would mean, that the alignments were not unique, and that is probably why I could not obtain ...
written 2.7 years ago by annadv7720
0
votes
1
answer
905
views
1
answer
Question: SAM-to-BAM: fatal exit code Error 139
... Dear All, I am analyzing DNAseq data. I obtained a SAM file by using "Map with BWA for Illumina data". However, when I try to transform that SAM file into BAM file, using "SAM-to-BAM" module, it stops and says: Galaxy attempted to build the BAM index with samtools 1.0+ but failed: [Errno 2] No suc ...
bam dnaseq sam written 2.7 years ago by annadv7720
0
votes
2
answers
3.8k
views
2
answers
Comment: C: Joining overlapping paired end reads
... Hi Bjoern, Thank you for suggesting to use PEAR from the Tool Shed - I've installed it and it working very well! I actually ended up not needing it for the project I intended to use it for, but it worked well on another set of data. Thank you!   Regards, Anna ...
written 3.1 years ago by annadv7720
0
votes
2
answers
3.8k
views
2
answers
Comment: C: Joining overlapping paired end reads
... Hi Guy, Thank you very much for your detailed reply. I agree with your points. Especially about having reads that are shorter than half the length of the insert. Unfortunately, I was not involved in the design of the experiment, and I was asked to work with the data, when it was already obtained. ...
written 3.1 years ago by annadv7720
0
votes
2
answers
3.8k
views
2
answers
Comment: C: Joining overlapping paired end reads
... Hi Guy, Thank you for your detailed reply! I am wondering whether the NGS:Picard (beta) > FASTQ to BAM tool will be able to deal with overlapping paired ends? Because I know that probably most of them are overlapping and by relatively long sequences (I think). Thank you!   Regards, Anna ...
written 3.1 years ago by annadv7720
0
votes
2
answers
3.8k
views
2
answers
Comment: C: Joining overlapping paired end reads
... Hi Bjoern,   Thank you very much for your suggestion! I will try PEAR for sure - I read about it, I just couldn't find it in the Tool shed for some reason. Thank you for providing the link!   Regards, Anna ...
written 3.1 years ago by annadv7720
3
votes
2
answers
3.8k
views
5 follow
2
answers
Joining overlapping paired end reads
... Dear All,   I have DNA sequencing data (targeted sequencing) produced by MiSeq. The size of the insert is 250bp, it was sequenced by using paired end reads and the reads are overlapping. I am planning to use velvet on Galaxy to perform de novo assembly. As I understand, velvet requires the input t ...
fastq_join galaxy overlapping paired end reads written 3.1 years ago by annadv7720 • updated 3.1 years ago by Guy Reeves1.0k
0
votes
0
answers
1.8k
views
0
answers
Installing and running Velvet assembler
... Dear All, We were trying to install and run the Velvet tool on our local Galaxy instance. However, we are unable to run the velveth tool: every time we try to do so, we receive the following message: "an error occurred with this dataset: Unable to run velveth: No such file or directory" To instal ...
velvet assembly written 3.1 years ago by annadv7720
0
votes
1
answer
2.1k
views
1
answers
Comment: C: Problem running Clustal 2.1 Multiple Sequences Alignment - an instance of 'std::
... Hello Jen, Thank you very much for the answer and for the links! I've seen some of the information before, but I'm going to check it more thoroughly. Thank you!   Regards, Anna ...
written 3.1 years ago by annadv7720

Latest awards to annadv77

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Joining overlapping paired end reads

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 122 users visited in the last hour