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55 results • Page
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Finding genes under positive selection in non-model species - Phylotranscriptomics approach ?
gene
ortholog
assembly
rna-seq
updated 21 hours ago by
Ram
41k • written 2.7 years ago by
sunnykevin97
▴ 970
0
votes
1
reply
688
views
Alternative tool for split'N'trim
SNP
Galaxy
Single-cell
RNA-seq
updated 21 hours ago by
Ram
41k • written 3.6 years ago by
aiswaryabioinfo
▴ 30
4
votes
11
replies
6.0k
views
6 follow
Installing and importing viennaRNA to python in windows
rna
python
viennarna
updated 12 hours ago by
Yun
• 0 • written 4.3 years ago by
ofek.schnitzer
▴ 30
1
vote
2
replies
2.3k
views
ERROR for Trinity abundance_estimates_to_matrix.pl
R
next-gen
RNA-Seq
software-error
updated 18 hours ago by
Ram
41k • written 5.4 years ago by
nasreenbano91
• 0
0
votes
7
replies
4.2k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq
alignment
software-error
next-gen
sequence
updated 18 hours ago by
Ram
41k • written 5.5 years ago by
nasreenbano91
• 0
55 results • Page
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Recent Votes
scRNA-seq CITE-seq-count bioinformatics
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ?
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ?
A: problem with chromosomes in michigan imputation server
Answer: Execute R command on specific termimal
rRNA decontamination of RNA-Seq reads (tool choice, introns etc)
Answer: Calculate GC content for entire chromosome
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Recent Replies
Answer: An issue with gtf file (ballgownrsem)
by
cucindarko51
• 0
I also encountered issues when running ballgownrsem with gff files. Ballgown object was created, there is no informations about TPM and FPK…
Answer: Scanpy Pearson residual PCA error
by
Maëlick
• 0
I had the same problems and then realize that I forgot the preprocessing! If you add this commands before running the PCA, it should work:…
Comment: Calculate GC content for entire chromosome
by
colindaven
5.8k
Try tripling your example seq length, see 20bp min region -l INT min region length to output [20]
Comment: Very low successfully assigned alignments with feature counts
by
GenoMax
136k
Is the genome/annotation from the same source i.e. Ensembl or so it appears?
Comment: Calculate GC content for entire chromosome
by
ATpoint
78k
What does this do? It's not documented well and does not work for me in terms of, it produces no output: cat foo.fa >chr1 GCGC…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Did you not see the last part in my comment above about how to get the sequence?
Comment: Execute R command on specific termimal
by
QX
• 0
Hi @atpoint Thank you for your answer!
Comment: Need help to find FASTA sequence from dbSNP
by
syedahumairagillani
• 0
Thank you for your response. Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
Answer: Calculate GC content for entire chromosome
by
colindaven
5.8k
In the meantime there is also seqtk gc https://github.com/lh3/seqtk seqtk gc Usage: seqtk gc [options] <in.fa> …
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
I have employed your above suggested approach for BQSR (latter one). I will try former approach too (that does not require reference vcf fi…
Comment: An issue with gtf file (ballgownrsem)
by
cucindarko51
• 0
Thank you! After using this tool, I figured out that **ballgownrsem** can be run successfully only with GFF files.
Answer: Execute R command on specific termimal
by
ATpoint
78k
This is not how HPCs work. Things do not happen automatically and independent of the job scheduler. If you want to work interactively o…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Using [**EntrezDirect**][1] you can find the location of this SNP: $ esearch -db snp -query rs1815739 | esummary | xtract -pattern Doc…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴ 10
For variant calling I followed following steps: **Step 1** I first made a vcf file to be used for quality score recalibration later > c…
Comment: Need help to find FASTA sequence from dbSNP
by
Pierre Lindenbaum
158k
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