User: Macspider

gravatar for Macspider
Macspider2.5k
Reputation:
2,540
Status:
Trusted
Location:
Vienna - BOKU
Twitter:
macspider_music
Last seen:
2 days, 4 hours ago
Joined:
1 year, 10 months ago
Email:
r*********@gmail.com

Posts by Macspider

<prev • 516 results • page 1 of 52 • next >
0
votes
1
answer
70
views
1
answers
Comment: C: Problems running variant calling (VC) GATK: SAM/BAM/CRAM file dedup.bam is malfo
... Both Devon and Genomax are right, because - at least my personal experience - it depends on your analysis. Are you running an analysis composed of different replicates/accessions/genomes/species, or are the data coming from one source and one replicate? - Many sources: add read groups that make ...
written 2 days ago by Macspider2.5k
3
votes
1
answer
70
views
1
answers
Answer: A: Problems running VC GATK: SAM/BAM/CRAM file dedup.bam is malformed
... > Error details: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups Your sam file doesn't have read groups. This is a common issue with GATK, as the program now wants the reads to be grouped for analysis purposes. You can ass ...
written 2 days ago by Macspider2.5k
0
votes
0
answers
172
views
0
answers
Comment: C: featurecounts more fragments than input read pairs
... If you isolate the read names of all the reads that have mapped, and then `sort | uniq` them, how many do you get? Chances that a multi-positional alignment is happening? ...
written 3 days ago by Macspider2.5k
0
votes
2
answers
54
views
2
answers
Comment: C: Getting a distinct set of Gene Ontology terms
... If you found my answer useful, upvote + mark it as answer, so the thread gets the "answered" status. (not because it's mine, just because it works like this here :D) ...
written 3 days ago by Macspider2.5k
1
vote
1
answer
60
views
1
answers
Comment: C: rsem-calculate-expression error message
... You also declare twice the `--star` argument in RSEM. That shouldn't be a problem, but since it seems that you're not super-solid on your command writing, perhaps check if every file you declare is in the folder you want it to be, check if every tag you added is exactly as it should be, and stuff li ...
written 3 days ago by Macspider2.5k
0
votes
2
answers
54
views
2
answers
Answer: A: Getting a distinct set of Gene Ontology terms
... Have a look at [GO.db][1]. In this R package, you can easily get PARENT, OFFSPRING and CHILDREN terms from a specified GO term. [1]: https://bioconductor.org/packages/release/data/annotation/html/GO.db.html ...
written 3 days ago by Macspider2.5k
1
vote
1
answer
60
views
1
answers
Comment: C: rsem-calculate-expression error message
... Is it normal that you have the same file specified in two arguments? `-o clean_2.fq.gz -O clean_2.fq.gz` ...
written 3 days ago by Macspider2.5k
0
votes
0
answers
61
views
0
answers
Displaying a controversial phylogenetic tree as a network to explicitate noise-generating branches
... Hi guys, I am not completely sure this question fits Biostars (if not: please point me to the right discussion forum!). I have generated a phylogenetic tree as a "consensus" of ~32,000 trees, each made from a different gene when compared with other species in a list I have. As the consensus tr ...
genome network tree phylogenesis convert written 7 weeks ago by Macspider2.5k
0
votes
2
answers
1.4k
views
2
answers
Comment: C: Technical replicates in RNAseq
... Comparative Genomics @ CRG, Barcelona http://www.crg.eu/en/toni_gabaldon ...
written 7 weeks ago by Macspider2.5k
1
vote
2
answers
1.4k
views
2
answers
Comment: C: Technical replicates in RNAseq
... The new comment in this discussion just made me realize that we had this thread ~10 months ago here, and now me and @grant are sitting next to each other in the same lab. XD Science: it's a small world! Apart from that, maybe it would be interesting to tell the readers what, in the end, you did w ...
written 7 weeks ago by Macspider2.5k

Latest awards to Macspider

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Good Question 9 weeks ago, asked a question that was upvoted at least 5 times. For Best way to compare two samples in a VCF file
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Popular Question 3 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 7 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Appreciated 7 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 8 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 8 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 8 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 9 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Scholar 9 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 10 months ago, created a question with more than 1,000 views. For Remove duplicates from reads: best practices?
Appreciated 10 months ago, created a post with more than 5 votes. For Best way to compare two samples in a VCF file
Scholar 12 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 12 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Popular Question 13 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Student 16 months ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 16 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
Voter 16 months ago, voted more than 100 times.
Scholar 16 months ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 725 users visited in the last hour