User: PAn

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PAn20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
2 years, 9 months ago
Joined:
3 years, 11 months ago
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p**************@gmail.com

Posts by PAn

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Extract a specific subsequence from a fasta file
... This works perfectly! ...
written 2.8 years ago by PAn20
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Extract a specific subsequence from a fasta file
... Hi, I have a 14 bp long sequence and I need to extract 10 bp +/- of this sequence from a list of fatsa sequences. Is there a tool that I can use to get the sequence string specific trimmed reads? The substring is GCACGAAGTTTTGC a sample read from the fasta file looks like - >58_1_uni01 ...
fatsa sequence extract written 2.8 years ago by PAn20 • updated 2.8 years ago by IP590
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Error in pysamstats
... Hi, I am trying to run pysamstats through a python script in jupyter, here is the code that I am trying to use : from __future__ import division, print_function import numpy as np %matplotlib inline import matplotlib.pyplot as plt import sklearn import pysam import p ...
python jupyter pysamstats written 2.9 years ago by PAn20 • updated 2.7 years ago by Biostar ♦♦ 20
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Comment: C: Count right and left mate pairs from Sam files
... flagstat would run on each sam file separately and i think will not compare based on read names between two files. I am trying to write a script to do this now. ...
written 3.0 years ago by PAn20
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Count right and left mate pairs from Sam files
... Hello, I have two separate left and right mate sam files from a sample's RNAseq data (these are unmapped sam files after running alignment both right and left mate fastq files) and I need to find out which of these reads come from pairs and which of these reads are left unmapped from either just ...
samtools sam written 3.0 years ago by PAn20 • updated 3.0 years ago by Brian Bushnell16k
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Finding downstream Gene Closest To A Given Location
... Hi, I am trying to find genes closest only downstream to a bed file. I am using bedtools closest -d -a Seq.bed -b Bed_GTF_neg.bed but it is giving me both upstream and downstream regions, is there anyway to get only the downstream regions? Thanks! ...
bedtools gene bedfile closest written 3.0 years ago by PAn20 • updated 3.0 years ago by harold.smith.tarheel4.5k
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Comment: C: GATK FastaAlternateReferenceMaker giving error
... Thanks a lot! This helps. ...
written 3.1 years ago by PAn20
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GATK FastaAlternateReferenceMaker giving error
... Hi, I am trying to run FastaAlternateReferenceMaker using an interval file but I am getting this warning whether I use the interval file or not. java -jar /local/scratch/aparihar/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R /PlasmoDB-24_Pfalciparum3D7_Genome.fasta -o Sample1.fast ...
gatk fastaalternatereferencemaker written 3.1 years ago by PAn20
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Duplicate miRNAs with different read counts in miRDeep2
... Hello, I am using miRDeep2 to calculate the read counts for a sequenced Mouse sample. I am using mature miRNAs and hairpin miRNAs from mirbase to calculate the read counts. I would expect unique miRNAs in the miRDeep2 result file - miRNAs_expressed_all_samples_sample.csv, but it gives different re ...
read counts mirna mirdeep mirdeep2 mirnas written 3.1 years ago by PAn20 • updated 3.1 years ago by benformatics1.2k
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Comment: C: How to compute RNA-Seq mapping stats for rRNAs?
... Thanks all! My group was using a script that would calculate the %exonic, %intronic and %intergenic by calculating the exonic bed file from the exon reads in gtf file, remove the exonic from the genic region etc and further calculate the intergenic, intronic etc using bedtools complement, merge etc. ...
written 3.2 years ago by PAn20

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