User: Pedro Morell

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Posts by Pedro Morell

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Error while visualizing FreeBayes.
... And this is the error message: Traceback (most recent call last): File "/galaxy-repl/instances/main/server/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py", line 40, in <module> main() File "/galaxy-repl/instances/main/server/lib/galaxy/datatypes/converters/inte   ...
written 2.7 years ago by Pedro Morell0
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Comment: C: Error while visualizing FreeBayes.
... #fileformat=VCFv4.1 ##fileDate=20160121 ##source=freeBayes v0.9.20 ##reference=/galaxy/data/canFam3/sam_index/canFam3.fa ##phasing=none ##commandline="freebayes --bam localbam_0.bam --fasta-reference /galaxy/data/canFam3/sam_index/canFam3.fa --vc ...
written 2.7 years ago by Pedro Morell0
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Comment: C: uploading bam file
... You may be pasting a view of the file you want to download instead of the actual file. You should try to get the actual url where your file is located so the Galaxy server can then download it from the source server. ...
written 2.7 years ago by Pedro Morell0
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Error while visualizing FreeBayes.
... Hi, I'm trying to visualize my FreeBayes results on IGV or UCSC, but while Galaxy tries to transferthe data, I get a Conflict warning, telling me that the tabix file couldn't be created, so my file can't be opened on those tools. This has something to do with my data, or am I missing somehting?   ...
freebayes tabix igv visualization error written 2.7 years ago by Pedro Morell0 • updated 2.7 years ago by Jennifer Hillman Jackson25k
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Error on mapping: my sliced sequence (for a certain gene) gets mapped 3mb away.
... I've sliced my original BAM files to my region of interest, and then transformed the sliced files into FASTQ to perform FASTQC. When I map again, both with BWA and Bowtie2, the new regios is 3 million bases away from the original region. What I'm doing wrong? ...
bam galaxy bowtie bwa mapping written 2.7 years ago by Pedro Morell0
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Comment: C: Extract gene sequence from BAM.
... I've been working with NGS:SAMtools and NGS:Picard. My first step was to pas from BAM to SAM, and then to FASTQ, a format I'm used to use, but I don't know how to get just the region I want to study. I'll try Slice BAM and see. Thanks. ...
written 2.7 years ago by Pedro Morell0
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Extract gene sequence from BAM.
... Hi, I have several BAM files with different samples of a chromosome and I want to end up with one file for each sample (two if they are paired) including only a certain region of that chromosome in order to study the variance. I've managed to convert the original BAM I'm using as a test into FASTQ, ...
bam gene sequence fastq written 2.7 years ago by Pedro Morell0 • updated 2.7 years ago by Jennifer Hillman Jackson25k

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