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scRNA-seq CITE-seq-count bioinformatics

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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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

what does it mean ?

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