Moderator: h.mon

gravatar for h.mon
h.mon24k
Reputation:
23,680
Status:
Trusted
Location:
Brazil
Last seen:
8 minutes ago
Joined:
6 years, 5 months ago
Email:
h***********@gmail.com

about me

Posts by h.mon

<prev • 3,523 results • page 2 of 353 • next >
2
votes
5
answers
127
views
5
answers
Answer: A: How to get the pathway-protein relationship?
... If you have a small number of entries, you can use the [KEGG Mapper – Convert ID][1], then clicking at the corresponding KEGG accession will take you to a page with lots of information, including the pathways that protein is involved. If you have a large number of entries, you can use the BioConduc ...
written 23 hours ago by h.mon24k
0
votes
1
answer
66
views
1
answers
Answer: A: visualize amino acid changes in genes that are positively selected after codeml
... The ETE3 toolkit wraps codeml and, in addition to performing selection tests, it produces some nice figures. It also has an interactive GUI mode where one can customize / explore the analyses and graphics. For examples, see: http://etetoolkit.org/documentation/ete-evol/ http://etetoolkit.org/docs/ ...
written 1 day ago by h.mon24k
1
vote
1
answer
71
views
1
answers
Answer: A: MiRdeep2 for paired-end RNA-seq?
... There is no option to input R1 and R2 fastq files because probably miRDeep2 author considered very unlikely someone would do paired-end sequencing for miRNA. Two suggestions: All reads should overlap, use some paired-end read merger (like BBMerge, PEAR or FLASH), and discard pairs that do not mer ...
written 1 day ago by h.mon24k
0
votes
0
answers
73
views
0
answers
Comment: C: How to calculate the mapping rate from BAM files generated from BWA
... `samtools flagstat`. See also `samtools stats` and `samtools idxstats`. ...
written 1 day ago by h.mon24k
2
votes
1
answer
61
views
1
answers
Answer: A: Can bedtools subtract support multiple files?
... To avoid intermediary files, you can chain the commands with pipes: bedtools subtract -a A.bed -b B.bed \ | bedtools subtract -a stdin -b C.bed \ | bedtools subtract -a stdin -b D.bed > only_A.bed Two notes: 1) I believe you meant `bedtools subtract -a temp2.bed –b D.bed > o ...
written 1 day ago by h.mon24k
0
votes
0
answers
131
views
0
answers
Comment: C: How to calculate percent identity from sam file?
... Just out of curiosity, why do you need this? ...
written 2 days ago by h.mon24k
0
votes
0
answers
48
views
0
answers
Comment: C: views on vgteam codebase on gituhb?
... **Why** do you need a rundown of the vg code base? Honestly, if you really are a "noob", start with something easier. ...
written 2 days ago by h.mon24k
1
vote
0
answers
131
views
0
answers
Comment: C: How to calculate percent identity from CIGAR string?
... The blog post [The history the MD tag and the CIGAR X operator][1] explains why the CIGAR shouldn't be used to calculate percent identity, but a TL;DR is: > First, CIGAR describes alignment, but sequence matches and mismatches are not indispensable properties of alignment. [1]: http://lh3.g ...
written 2 days ago by h.mon24k
0
votes
1
answer
56
views
1
answers
Answer: A: miRDeep2 - same micro seq but different coordinates
... The phenomenon you are observing - particularly (1.) - is the presence of miRNA isoforms, or isomiRs. The simplest approach is to sum all isomiRs and then perform differential expression analysis. However, isomiRs may have biological importance, and it may be worth to perform the analysis at the is ...
written 3 days ago by h.mon24k
0
votes
1
answer
88
views
1
answers
Comment: C: Human genome annotation
... Do you **really** need to annotate the human genome? It is probably the best annotated eukaryotic genome. And why are you using a *Drosophila melanogaster* (Dmel.BDGP5.25.62.DEXSeq.chr.gff) annotation? ...
written 3 days ago by h.mon24k

Latest awards to h.mon

Teacher 20 hours ago, created an answer with at least 3 up-votes. For A: RNA-seq: Can we obtain distances between samples of different experiments?
Scholar 20 hours ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Commentator 1 day ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: convert STAR ReadsPerGene.out.tab to Deseq2 count table
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: RNA-seq: Can we obtain distances between samples of different experiments?
Scholar 4 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Commentator 4 days ago, created a comment with at least 3 up-votes. For C: STAR align multiple files
Appreciated 8 days ago, created a post with more than 5 votes. For Where did EMBOSS go?
Scholar 9 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: RNA-seq: Can we obtain distances between samples of different experiments?
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: RNA-seq: Can we obtain distances between samples of different experiments?
Scholar 9 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: RNA-seq: Can we obtain distances between samples of different experiments?
Scholar 9 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: RNA-seq: Can we obtain distances between samples of different experiments?
Appreciated 16 days ago, created a post with more than 5 votes. For Benchmarking bioinformatics tools
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Are secondary alignments used by any tool?
Scholar 17 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Scholar 23 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Scholar 28 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Teacher 28 days ago, created an answer with at least 3 up-votes. For C: Identify insertions with IGV
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Are secondary alignments used by any tool?
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Are secondary alignments used by any tool?
Scholar 28 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them
Scholar 29 days ago, created an answer that has been accepted. For A: Find bams with identical names and merge them

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2057 users visited in the last hour