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Showing top results for tag: Trim • reset
1
vote
3
replies
295
views
cutadapt not working when calling in a bash code with qsub
qsub trim cutadpat
updated 23 days ago by 85k • written 23 days ago by • 0
5
votes
6
replies
1.4k
views
Trimming nanopore reads
trim nanopore
updated 9 months ago by ▴ 150 • written 9 months ago by ▴ 10
0
votes
2
replies
831
views
trimming primers using iVar
trim iVar primer
updated 12 months ago by 146k • written 12 months ago by • 0
1
vote
2
replies
699
views
mac trimmomatic problem.
trim RNA-seq
updated 23 months ago by 44k • written 23 months ago by ▴ 10
4
votes
4
replies
912
views
Should I skip trimming, and do deseq2 directly if fastqc only shows adapters.
deseq2 trim fastqc
updated 24 months ago by 85k • written 24 months ago by • 0
0
votes
0
replies
428
views
WGS trimming end of the reads for specific bp before alignment and call somatic variants
read trim WGS somatic variant
2.0 years ago by woongjaej ▴ 30
0
votes
0
replies
688
views
Adapter sequences left after trimming small RNA seq data with TrimGalore!
Trim small miRNA RNA Galore
2.1 years ago by ntsopoul ▴ 60
0
votes
0
replies
451
views
Difference between trim galore report and Fastqc pre trimming
trim galore report
2.3 years ago by Luern • 0
2
votes
5
replies
1.2k
views
How can I randomly choose and delete a set number of nucleotides from a fasta file?
random fasta trim
2.4 years ago by Jonathan ▴ 20
3
votes
3
replies
875
views
Help with the reads filtering process
filtering trim
2.4 years ago by valentinavan ▴ 50
5
votes
2
replies
663
views
trim fasta header, remove after hash (#)
header fasta hash trim
updated 2.4 years ago by 21k • written 2.4 years ago by ▴ 50
0
votes
7
replies
1.2k
views
Complex adaptor trimming
sequencing Trimming galore trim
updated 2.6 years ago by ★ 2.2k • written 2.6 years ago by • 0
3
votes
4
replies
1.1k
views
Do I need to trim the reads on samples with <0.2% adapter content?
adapter map fastqc trim
2.8 years ago by compuTE ▴ 140
0
votes
1
reply
1.0k
views
Anyone could help me with cutadapt?
Cutadapt trim primer
updated 3.0 years ago by ★ 2.7k • written 3.0 years ago by • 0
0
votes
0
replies
648
views
Trimming Nextera adapter from scRNA paired reads with different length
scRNA Adapter trimming Trim Galore Nextera
3.2 years ago by almogangel • 0
5
votes
2
replies
751
views
When NOT to trim adaptors?
exome trim adaptors
3.3 years ago by rtho ▴ 20
1
vote
10
replies
3.1k
views
Trimming customed adaptor sequences with trimmomatic
trimmomatic trim illumina exon
updated 3.4 years ago by 44k • written 3.6 years ago by ▴ 80
1
vote
3
replies
2.1k
views
Trim_galore with gnu parallel
parallel trim_galore RNA-Seq trim fastq
3.7 years ago by francesca3 ▴ 150
0
votes
4
replies
1.7k
views
Trim 3' ends from single-end reads
trim 3' end single-end read
4.0 years ago by Maria • 0
2
votes
1
reply
1.1k
views
Trimmomatic trims most of the reverse strand
fastq trim trimmomatic bwa
updated 4.1 years ago by 146k • written 4.1 years ago by ▴ 180
1
vote
2
replies
1.6k
views
ATAC-Seq kmer removal
ATAC-Seq fastqc trim kmers cutadapt
updated 4.7 years ago by 35k • written 4.7 years ago by ▴ 30
2
votes
3
replies
1.9k
views
flexbar for many files
RNA-Seq flexbar adapter trim
5.0 years ago by charadriussp • 0
0
votes
4
replies
3.8k
views
How to trim primers with cutadapt from .fastq.gz file?
cutadapt primer trim
updated 16 months ago by 44k • written 5.6 years ago by • 0
10
votes
7
replies
21k
views
8 follow
Trimming fastq with quality
RNA-Seq fastx fastq trim FastQC
updated 2.9 years ago by 44k • written 10.2 years ago by ▴ 120
17
votes
7
replies
10k
views
6 follow
How to speed up trimming using trim galorer
RNA-Seq fastq trim
updated 2.7 years ago by ▴ 60 • written 5.8 years ago by ▴ 100
0
votes
3
replies
1.1k
views
Trim fasta to a specific gene location
fasta bash trim alignment sequence
6.0 years ago by James ▴ 20
5
votes
6
replies
2.2k
views
Have bbduk retain quality scores in output after kmer trimming
trim primer bbmap
6.1 years ago by caverill ▴ 40
1
vote
4
replies
4.3k
views
trimming RNA-seq reads with adapter sequence?index? using trimmomatic
RNA-Seq trimmomatic adapter trim
updated 6.9 years ago by ▴ 840 • written 6.9 years ago by ▴ 30
4
votes
8
replies
3.5k
views
Trimming reads with prinseq
prinseq reads preprocessing qual trim
7.0 years ago by deepti1rao ▴ 50
6
votes
7
replies
3.2k
views
error while using cutadapt
cutadapt trim
updated 7.0 years ago by ★ 2.5k • written 7.0 years ago by ▴ 600
7
votes
9
replies
8.2k
views
trimming nano pore reads based on quality score.
nanopore trim
updated 7.0 years ago by 47k • written 7.0 years ago by ▴ 600
1
vote
7
replies
2.2k
views
Trim read-specific adapter in paired-end reads
adapter trim
7.0 years ago by Nicolas Rosewick 11k
0
votes
6
replies
2.2k
views
Is it possible/recommended to trim RNA-Seq reads to a specific length
trim RNA-Seq chimeraScan STAR-Fusion
updated 7.5 years ago by 20 • written 7.7 years ago by ★ 4.1k
1
vote
4
replies
2.8k
views
trimming reads from miseq
trim miseq fastqc duplcation level
7.6 years ago by mary ▴ 10
1
vote
3
replies
4.6k
views
Trim Reads From BAM files
BAM bamUtil Trim
updated 7.6 years ago by 20 • written 7.7 years ago by ▴ 250
2
votes
7
replies
3.2k
views
trim special lenght from special tile in a fastq file
tile trim per tile sequence quality
updated 7.7 years ago by ★ 2.8k • written 7.7 years ago by ▴ 10
1
vote
3
replies
5.4k
views
How to trim adapters and remove polyA tails from QuantSeq 3' FWD data
RNA-Seq quantseq trim poly-A tails
7.7 years ago by Chloe • 0
3
votes
2
replies
4.1k
views
How to clean bad tiles from Illumina reads?
RNA-Seq illumina fastqc quality trim
updated 7.7 years ago by ★ 5.0k • written 7.7 years ago by • 0
2
votes
2
replies
3.0k
views
Use Bowtie to trim reads in fastq files
bowite trim
updated 7.8 years ago by 20k • written 7.8 years ago by ▴ 70
1
vote
8
replies
1.6k
views
trimming more than two paired mates
trim fastq
8.0 years ago by igor 13k
3
votes
3
replies
3.8k
views
Should I trim both R1 and R2 if only R2's quality is poor?
trimming trim reads fastqc
updated 8.4 years ago by 13k • written 8.4 years ago by 5.9k
14
votes
6
replies
6.3k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 19 months ago by 44k • written 8.4 years ago by 15k
6
votes
5
replies
6.9k
views
Interpretation of FASTQC results - do I need to trim my sequence?
Assembly sequencing fastqc trim illumina
updated 8.6 years ago by ★ 2.5k • written 8.6 years ago by ▴ 10
6
votes
2
replies
3.4k
views
Fa list for illumina sequencing adapters
adapter sequencing trim illumina
updated 2.8 years ago by 44k • written 9.0 years ago by ★ 9.5k
0
votes
3
replies
3.2k
views
Cutadapt list of adapter
trim cutadapt
updated 2.1 years ago by 44k • written 9.1 years ago by ▴ 40
0
votes
2
replies
2.4k
views
Trim barcode 3'
primer trim cutadapt barcode
updated 2.1 years ago by 44k • written 9.1 years ago by ▴ 40
3
votes
8
replies
6.2k
views
Trim sequences in FASTA file from sanger sequencing
sanger sequencing trim NNNN
10.6 years ago by merajazizmeraj ▴ 20
47 results • Page 1 of 1
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The Biostar Herald for Friday, November 01, 2024
The Biostar Herald for Friday, November 01, 2024
Clustering and dynamic tree cutting
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
Answer: Coverage data for TCGA BAM files
Answer: Coverage data for TCGA BAM files
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Recent Replies
Comment: Are there any preferred trajectory/pseudotime analyses that do not require an ar by Jean-Karim Heriche 27k
Maybe consider seriation/ordination as an alternative.
Comment: dedup STAR transcriptome file using umi_tools by i.sudbery 20k
There are bulk protocols that include UMIs. Lexogen's CORRAL kits for example. Or NEB's NEBNext UMI adaptors.
Answer: dedup STAR transcriptome file using umi_tools by Michael 55k
I am quite sure that you cannot use UMI_tools to deduplicate bulk RNA-seq. The different oligo adapter sequences on each bead introduce UMI…
Answer: dedup STAR transcriptome file using umi_tools by i.sudbery 20k
I don't know if any reason you shouldn't be able to index the bam produced by STAR, although you will need to sort them first.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by wangziwei0010 ▴ 30
Hi ATpoint, Thank you for your though provoking answer. Big fans! Actually I have some normal cells in each sample, and I found good mixt…
Answer: Differential binding analysis between different TFs by Ming Tommy Tang ★ 4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/ also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session by Dunois ★ 2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
Comment: PyDeseq2 - InvalidIndexError by Dunois ★ 2.7k
You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra by Dunois ★ 2.7k
Expand your search by searching these (two) sequences against other sets of sequences. That said, why does it feel like this is an [XY pro…
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It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I'm wondering if this could work: `bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l` …
Comment: GISTIC 2.0 parameter change not happening by Ram 44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data by allingt • 0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
example vcf: ``` CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4 chr1 100 . C …
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