User: teresayahu

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teresayahu0
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Posts by teresayahu

<prev • 6 results • page 1 of 1 • next >
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mutation type probability
... In the mutation signatures in cosmic, http://cancer.sanger.ac.uk/cosmic/signatures, there is a figure with barplot describing the distribution of mutation type in each signature. In the plot, the y-axis is the value of Mutation Type Probability. Is there a link to download the exact value of mutatio ...
mutation signatures cosmic written 3 months ago by teresayahu0
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about python module aln
... Hi, I am using script remove_mapping_reads.py from EBV portal https://ebv.wistar.upenn.edu/tools.html. In running the script there is an error: Traceback (most recent call last): File "remove_mapping_reads.py", line 4, in import sys, os, bisect, time, pysam, aln, gzip ModuleNotFoundError: ...
python ebv module written 6 months ago by teresayahu0
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Comment: A: samtools mpileup error
... Thanks! both the bam and reference files are using the '1'. Is there a way that I can change bam notation from '1' to 'chr1'? ...
written 9 months ago by teresayahu0
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samtools mpileup error
... I am using samtools function mpileup to get reads in sites. The command I used is: samtools mpileup -l hg19.position -f hg19.fa -Q 20 -q 20 -I file.bam in the command, hg19.position is position-based site file. When running these is an error printed on screen: ... [E::faidx_fetch_seq] The s ...
software error assembly next-gen sequence written 9 months ago by teresayahu0
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Comment: C: How to retrieve hard clipped reads
... Exactly. I don't have the fastq files and only have bam file. ...
written 9 months ago by teresayahu0
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How to retrieve hard clipped reads
... Hi, Is there a way to retrieve the part of reads that has been hard clipped and discarded in bam files? Thanks! ...
alignment written 9 months ago by teresayahu0 • updated 9 months ago by d-cameron1.8k

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