User: yhoogstrate

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yhoogstrate60
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Netherlands
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6 hours ago
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3 years, 5 months ago
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Posts by yhoogstrate

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Estimation of RNA-seq protocol from bam files
... If you make a discordant alignment and browse to CDR1 (circRNA) you will find quite a number of back-splice junctions in the ribo-minus/random primed data and not in the polyA+. I must admit that I only know this works in human data and I am not sure if that's what you're aiming for. Intronic conte ...
written 26 days ago by yhoogstrate60
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Comment: C: Convert 2 SE bam to PE bam (alignment BWA mem)
... Pierre gives a good suggestion. Merging will most likely result in incorrect values that affect things such as stranding and which read belongs to which, in later analysis. These SAM flags will become incorrect unless they will be 'fixed' on top of a merge: - read paired (0x1) - read mapped in p ...
written 11 months ago by yhoogstrate60
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Comment: C: Subsampling one bamfile multiple times?
... I am not sure if this is what you are looking for, but the -s argument does support multiple seed values: *-s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the fraction of templates/read pairs to keep; INT part sets seed)* Changing the seed will result in a different (but reproduci ...
written 11 months ago by yhoogstrate60
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Answer: A: Merging two fastq.gz files
... Is this what you're looking for maybe?: ` for rf in 22[71-94]*R1_001.fastq.gz; do cat $rf >> 22"${71-94}"_merged_R1_001.fastq.gz ; done` zcat extracts, which is unnecessary as you dump it into a .gz file. Also, `>>` appends, `>` overwrites, of which appending seems what you need? ...
written 22 months ago by yhoogstrate60
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Answer: A: HOw to merge multifasta sequence into a single sequence having only one header?
... `grep -v '^>' in.fa > out.fa` if in.fa = >chr1 ttttccccaaaagggg >chr2 ACTGACTGnnnnACTG >chr3.1 ACTGACTGaaaac >chr3.2 ACTGACTGaaaacc >chr3.3 ACTGACTGaaaaccc >chr4 ACTGnnnn >chr5 nnACTG then out.fa becomes: tttt ...
written 2.1 years ago by yhoogstrate60
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Answer: A: How to count fasta sequences efficiently using (or not ) biopython
... You could take a look at this python lib: https://github.com/mdshw5/pyfaidx. It makes use of .fai files or may generate one. It is also compatible with gziped fasta's. ...
written 2.1 years ago by yhoogstrate60
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Comment: C: Regarding Sam output
... The file you refer to has been split up over two files somewhere in the last one or two years. Tags are now desribed in here: https://samtools.github.io/hts-specs/SAMtags.pdf ...
written 2.2 years ago by yhoogstrate60
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Answer: A: STAR GenomeIndex output (which is the BAM file?)
... genomeGenerate doesn't prdoce a SAM/BAM file, STAR only produces one if you run it in normal mode upon some FASTQ/FASTA data and the generated index. ...
written 2.3 years ago by yhoogstrate60
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Answer: A: Faster (perhaps random) access to BAM files (for collecting statistics like aver
... If your indexes are in place you might consider parsing the output of `samtools idxstats`. ...
written 2.3 years ago by yhoogstrate60
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Answer: A: Lift-over on a VCF
... CrossMap can do the trick as well - http://crossmap.sourceforge.net/ ...
written 2.3 years ago by yhoogstrate60 • updated 5 months ago by zx87549.0k

Latest awards to yhoogstrate

Supporter 6 months ago, voted at least 25 times.
Scholar 2.3 years ago, created an answer that has been accepted. For A: Faster (perhaps random) access to BAM files (for collecting statistics like aver

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