User: mary

gravatar for mary
mary0
Reputation:
0
Status:
New User
Last seen:
3 years ago
Joined:
3 years, 9 months ago
Email:
m**********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by mary

<prev • 15 results • page 1 of 2 • next >
0
votes
0
answers
553
views
0
answers
logical operators in Modelseed GPR
... Hi there I have been working with Modelseed driven network reconstructs and have problems understanding the logical operator and parenthesis' meanings in some reaction's GPR (file in xls format); (geneA and geneA) the product of geneA is a homodimer? (geneA or geneA) the produced prot ...
logical operator modelseed gpr written 3.1 years ago by mary0
0
votes
2
answers
2.6k
views
2
answers
Comment: C: search for low coverage regions on bam file
... the original bam file has some mapped scaffolds, each with a defined length. I want to have low coverage regions but not when they are near the beginning or at the end of a scaffold. for example, if scaffold 1 is 2000 bp and has a low coverage region at 4-26 bp or another one at 1900-190 bp these r ...
written 3.6 years ago by mary0
0
votes
2
answers
2.6k
views
2
answers
Comment: C: search for low coverage regions on bam file
... Can this code be modified in a way that low coverage regions of both ends in each contig would not be listed? ...
written 3.6 years ago by mary0
0
votes
2
answers
156
views
2
answers
Comment: C: How to find mismatches in an assembly
... I'm working on genomic DNA, not transcripts and I mapped them with bowtie2, then sort and index by samtools ...
written 3.6 years ago by mary0
0
votes
2
answers
156
views
2
answers
Comment: C: How to find sequencing errors
... Dear friends. I am working on de novo assembly of a prokaryotic cell. What I mean, is alignment mismatches. 40% of mapped reads don't show the same nucleotides as what has been predicted to be in the resulting genome. Look at the situation in the beginning of this contig for example:![contig][1] ...
written 3.6 years ago by mary0
0
votes
2
answers
2.6k
views
2
answers
Comment: C: search for low coverage regions on bam file
... Thanks, neat and helpful! just the -i option should be removed ...
written 3.6 years ago by mary0
0
votes
2
answers
2.6k
views
2
answers
Comment: C: search for low coverage regions on bam file
... As much as I know, when working with BAM files, you do not need to specify genome file. ...
written 3.6 years ago by mary0
3
votes
2
answers
2.6k
views
2
answers
search for low coverage regions on bam file
... Trying to find regions with a coverage less than 9 in a BAM file, I used: bedtools genomecov -bga -ibam infile.bam | awk '$4<9' > lessthan9cov.bed The output file is something like: scaffold1 12861 12866 7 scaffold1 12866 12877 1 scaffold1 12877 12896 3 scaffold1 31 ...
bedtools genomecov coverage awk written 3.6 years ago by mary0 • updated 3.6 years ago by Pierre Lindenbaum131k
0
votes
0
answers
1.6k
views
0
answers
Comment: C: trimming reads from miseq
... thank you but did you have a look at the reports? Shouldn't I worry about parameters like duplication rate or per base sequence content etc.? ...
written 3.6 years ago by mary0
1
vote
0
answers
1.6k
views
0
answers
trimming reads from miseq
... Hi I am going to make a reliable draft genome of a cultured bacteria. This is my FastQC report on Miseq reads from a genome sequencing project of bacteria prior to any trimming: http://www.yumpu.com/en/document/view/58094396/r1-a The original sequencing is a paired end but to focus on my problem, ...
duplcation level miseq trim fastqc written 3.6 years ago by mary0

Latest awards to mary

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1236 users visited in the last hour