User: Iñigo Prada

gravatar for Iñigo Prada
Iñigo Prada330
Reputation:
330
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
2 hours ago
Joined:
11 months, 2 weeks ago
Email:
p*******@hotmail.es

I am a second year Bioinformatics student and a student assistant/ Bioinformatician at the University of Copenhagen

Posts by Iñigo Prada

<prev • 71 results • page 1 of 8 • next >
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Gene expression sperm database
... Hi Biostars! I have a set of structural variants identified in sperm, and I wanna see if there is a relationships between the mutation rate of those variants and gene expression to see if transcription correlates with mutation rate. To to so, I have gone to and [EBI expression atlas][1] and [GTEx][ ...
gtex rna-seq written 17 days ago by Iñigo Prada330
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Comment: C: Where can I download whole genome sequencing data and variant calling result of
... https://www.ncbi.nlm.nih.gov/sra ...
written 18 days ago by Iñigo Prada330
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Comment: C: problems installing samtools and bcftools simultaneously
... What is the error message? ...
written 19 days ago by Iñigo Prada330
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Answer: A: Extract R2F1 reads
... I am the OP,finally I have been able to do this efficiently with pysam doing the following: NB: The input is a query name sorted bam, this allows to iterate the bam faster bam = pysam.AlignmentFile("/path/to/input/input.bam", "rb") tandem_dups = pysam.AlignmentFile("/path/to/output/output. ...
written 20 days ago by Iñigo Prada330
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Comment: C: Extract R2F1 reads
... > Or you haven't been able to try at all? I would not have asked if I haven't tried :) I have try both samtools and pysam. With samtools, I have try to extract them using the bitwise flag (145 flag) but the output is not the expected one, it includes reads supporting inversions (<- <-, F ...
written 21 days ago by Iñigo Prada330
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Extract R2F1 reads
... Hi everyone! I want to extract all reads from a bam file that have the orientation R2F1, as in the following image: ![image][1]. I have try to do this with samtools or pysam and I have not been able. I have seen in other posts some scripts for doing this with C++ or java, but, besides I don't k ...
samtools pysam structural variation written 22 days ago by Iñigo Prada330
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Comment: C: Aligning with huge insertion variations
... which software have you tried? I would expect bwa-mem to be able to handle those alignments with the 'SA' tags ...
written 24 days ago by Iñigo Prada330
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Comment: C: How to extract the circRNA sequences based on the the back-spliced junctions det
... Are you sure that the output is from circexplorer? circexplorer outputs exon information. Then, you could code a little bit or use existing utilities for dealing with that ...
written 25 days ago by Iñigo Prada330
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Comment: C: pysam truncated file error
... yeah, then to short the query name length is your option. Another option could be to downgrade Htslib and pysam. ...
written 26 days ago by Iñigo Prada330
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Comment: C: pysam truncated file error
... This is a problem with htslib-1.4 see this [github issue][1]. It will probably truncate the bam file, but trying to modify the query names longer than 252 with awk might help you. What do you wanna do with the bam file in the downstream analysis? ( I ask this to provide a useful answer) [1]: htt ...
written 27 days ago by Iñigo Prada330

Latest awards to Iñigo Prada

Scholar 20 days ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Scholar 5 weeks ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Supporter 5 months ago, voted at least 25 times.
Scholar 7 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.

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