User: Juan Ledesma

gravatar for Juan Ledesma
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United Kingdom
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1 year, 1 month ago
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j********@yahoo.es

Posts by Juan Ledesma

<prev • 10 results • page 1 of 1 • next >
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How to remove soft clipping reads
... Hi Does anyone know a way or a tool to remove soft and hard clipping reads from the sam file using Galaxy? Thanks ...
samtools sam written 3 months ago by Juan Ledesma0 • updated 3 months ago by Jennifer Hillman Jackson23k
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Answer: A: Mismatch penalty in BWA
... Thanks for your comments Jen, it is very useful for me. Cheers Juan ...
written 3 months ago by Juan Ledesma0
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Mismatch penalty in BWA
... Hi Does anyone know the highest mismatch penalty that I can set to get a more selective alignment in BWA? I would like to map my reference sequence only to the reads that are identical and exclude those ones that can be similar but no identical to the reference sequence. I am trying to identify ...
mapping alignment bwa written 3 months ago by Juan Ledesma0
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Extract reads from BAM file
... Hi I have a BAM file with all the reads aligned to the reference sequence that I used to map them. I would like to extract all the reads from the BAM file in order to get the nucleotide sequence aligning to the reference sequence for every single read. If I use bam to sam tool, I will get the or ...
bam reads written 12 months ago by Juan Ledesma0 • updated 12 months ago by Jennifer Hillman Jackson23k
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Comment: C: error with sam to bam conversion
... Hi Mo I have tried the tool that you have suggested and it seems that I get unique mapping reads. Thank you However, i think it will be very difficult to use this approach to analyse viral quasispecies or close related viral populations in the same sample using Galaxy. ...
written 12 months ago by Juan Ledesma0
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Answer: A: error with sam to bam conversion
... Hi Dannon This is the process I followed: 1) I generated a SAM file after mapping two different reference sequences, named as RS16000389_V3_Ref_1 and Ref_2, simultaneously to my FASTQ files and removed unmapped reads and secundary/suplementary alignments. 2) I used the tool "Filter data on any col ...
written 12 months ago by Juan Ledesma0
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error with sam to bam conversion
... Hi I am trying to convert my SAM file to BAM file but I always get this error message *Error extracting alignments from (dataset_487178.dat), [sam_header_read2] 2 sequences loaded. Parse error at line 3: missing colon in auxiliary data* Does any one know what it means? Thanks in advance Juan ...
bam sam written 12 months ago by Juan Ledesma0
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Answer: A: Mapping using multiple reference sequences
... Hi Mo Many thanks for your advice. I managed to filter the reads aligning to each sequence using the filter tool and the specific identifiers for each one. Thanks again Juan ...
written 13 months ago by Juan Ledesma0
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Answer: A: Mapping using multiple reference sequences
... Hi Basically what I do is using a single file where I have the two fasta sequences that I am interested to use as reference sequences and I map the FASTQ files to it using BWA. Afterwards I filter the reads to remove the unmapped ones and I get a sam file which includes the reads mapping both refe ...
written 13 months ago by Juan Ledesma0
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Mapping using multiple reference sequences
... Hi I am using BWA to map my FASTQ files against two different reference sequences (V3-1 and V3-2) simultaneously on Galaxy to see the reads belonging to each sequence. Once I've got the SAM file I would like to filter the mapped reads to generate two BAM files in order to get one file with the rea ...
reference mapping samtools bwa bam written 13 months ago by Juan Ledesma0

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