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1500 questions
7
votes
1 answer
Reject reads with low quality bases from a Bam file through pysam
I have a code below:
def FilterReads(in_file, out_file):
def read_ok(read):
"""
read_ok - reject reads with a low quality (<5) base call
read - a PySam AlignedRead object
returns: True if the read is ok
"""
if any([ord(c)-33…
Ammar Sabir Cheema
- 951
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- 20
7
votes
2 answers
differential gene expression complex design no replicates
We have an experimental design as seen below
Where we administered drug at 0 min for each mouse genotype and took them down at given below intervals. wt and ko mouse models were administered only with the vehicle which would be our negative…
novicebioinforesearcher
- 771
- 1
- 6
- 15
7
votes
1 answer
Filtering bases based on phred qualities with pysam
Is there a way to filter bases in BAM files based on phred quallities through python's pysam ?
I have a code here that
Takes the nucleobases per position from a BAM file using pysam's pileup function
Saves it in ReverseList and ForwardList based on…
Ammar Sabir Cheema
- 951
- 7
- 20
7
votes
1 answer
insert size pre and post trimming
I have a problem here with my rna seq data:
Sequencing details:
rRNA was removed, followed by cDNA preparation and generation of stranded libraries using the TruSeq Stranded Total RNA Sample Prep Kit. Sequencing performed on the HiSeq2500 platform…
novicebioinforesearcher
- 771
- 1
- 6
- 15
7
votes
3 answers
Visualization tools for 3C/Hi-C long-range interaction data?
I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples.
After viewing it in the UCSC genome browser, I have confirmed that it does not overlap any annotated gene…
Ben D.
- 397
- 1
- 10
7
votes
3 answers
Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file
As the title summarizes, I am trying to:
Read a PDB file (for example, 1enh.pdb).
Extract the backbone dihedral angles (phi, psi).
Modify the dihedral angles (phi, psi) arbitrarily (for example, replace them with np.random.uniform(-np.pi, np.pi,…
epsilone
- 125
- 6
7
votes
2 answers
Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?
I have a project to write in Python that requires to write a function that given degenerate DNA sequence (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all unambiguous sequences represented by the given…
Ke Keiss
- 71
- 2
7
votes
4 answers
Are variant calling files personally identifiable information?
This question is to be read in the context of data protection. It seems to be common understanding that the whole genome sequence of an individual is personally identifiable, non-anonymizable information: if you possess the whole genome sequence,…
Eekhoorn
- 172
- 6
7
votes
1 answer
How to represent random sequence elements in SBOL?
In our lab, we work with synthetic biology components with partially random sequences (similar to work in directed evolution). So, for example, we have a plasmid design with several components, including one protein coding sequence that will be…
David Ross
- 173
- 5
7
votes
2 answers
How do I write tests for a snakemake pipeline?
I've been playing with snakemake, which is really powerful, however, I'd like to create a 'unit test' for the whole pipeline. e.g. a way to call the pipeline that tests that all the rules work together, all the steps complete, etc.
I assumed I could…
Dan Bolser
- 470
- 2
- 10
7
votes
3 answers
How to modify execution orders for Snakemake?
My goal is to process two samples, S1 and S2, using two rules, step1, step2.
The Snakemake file is like:
SAMPLES = ['S1', 'S2']
rule all:
input: expand("{sample}.done", sample = SAMPLES)
rule step1:
input: "{sample}"
output:…
zhanxw
- 213
- 1
- 6
7
votes
1 answer
What does it mean if aligned genomes are not of the same length?
I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used:
progressiveMauve --output=outputfile --disable-backbone chl189.fas chl17415.fas chl50083.fas chlTAMOak81.fas
At the end, the resulting aligned…
Anthony Guterres
- 95
- 3
7
votes
5 answers
Convert FASTA to FASTQ with dummy quality scores
I have a FASTA file which I would like to convert into FASTQ format as the tool I want to use my data in requires it in FASTQ format. So dummy quality scores are fine.
Note: I am not using any functionality of the tool that will require the quality…
Michael Hall
- 663
- 4
- 11
7
votes
4 answers
How to convert gff to gtf?
My annotation file is in .gff format. I would like to convert it to .gtf format or to know if there is a way to directly download the annotation file in .gtf format?
I am working on sequences from the P Falicparum 3D7.
Diango
- 161
- 1
- 1
- 4
7
votes
2 answers
Understanding the significance of BLAT score calculations for read fragment alignment
I'm attempting to reconstruct the read fragments that form a hit to a target, excluding/skipping gaps. BLAST's outfmt 6, and alternatives such as Diamond's M8 format only give the number of gap opens on the alignment. One can't just use the start…
Sam Nicholls
- 782
- 4
- 16