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12
votes
5
replies
288
views
Remove duplicates in fasta files based on a specific value with awk
sort fasta sed awk
updated 13 days ago by 17k • written 13 days ago by ▴ 10
12
votes
5
replies
354
views
how to sort the rows of a file as a matrix?
cut sort awk sed matrix
updated 11 weeks ago by ★ 3.8k • written 11 weeks ago by • 0
1
vote
2
replies
174
views
Sort blast result in format 6 by first column
blast unix commands Sort result
12 weeks ago by Elene • 0
4
votes
4
replies
814
views
Samtools sort: too many open files error
samtools sort
updated 5 months ago by ▴ 700 • written 6 months ago by ▴ 30
3
votes
5
replies
864
views
I could not load GTF data at IGV("Could not create index file") Please help me :)
gtf igvtools igv sort index
updated 5 months ago by 106k • written 5 months ago by • 0
22
votes
20
replies
3.1k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam markduplicates sort bqsr Tool
7 months ago by Charlotte.Herzeel ▴ 150
5
votes
4
replies
361
views
Get the top X number of lines per unique value in one column, once you've sorted a text file using 'sort'
bash shell sort
updated 8 months ago by 106k • written 8 months ago by • 0
6
votes
4
replies
332
views
How to sort blast results by a minimum % of identical matches?
blast output sort identical matches
updated 10 months ago by 49k • written 10 months ago by ▴ 60
1
vote
12
replies
532
views
Error while attempting to create a VennDiagram with bcftools stats
bcftools sort venndiagram
updated 11 months ago by 20 • written 13 months ago by ▴ 20
1
vote
4
replies
358
views
Decreasing only numeric columns (more than one) in a dataframe with character and numeric column
sort decreasing R RNA-Seq
updated 12 months ago by 34k • written 12 months ago by ▴ 50
2
votes
0
replies
1.1k
views
Tutorial: Sorting GFF/GTF files
annotation gff gtf sort Forum Tutorial
14 months ago by Juke34 ★ 6.3k
3
votes
4
replies
1.0k
views
sambamba-sort: Error reading BGZF with BAM file
software error sort sambamba
updated 16 months ago by 53k • written 16 months ago by ▴ 570
4
votes
7
replies
450
views
sorting for bedtools genomecov doesn't work properly
bedtools sort bedpe RNA-Seq bedgraph
updated 18 months ago by 77k • written 18 months ago by ★ 1.6k
31
votes
8
replies
70k
views
samtools sorting and indexing
samtools index sort
updated 20 months ago by ▴ 280 • written 4.2 years ago by ▴ 80
0
votes
2
replies
302
views
How to get unique counts saved in a file
linux Sort Awk Unique counts
updated 21 months ago by 106k • written 21 months ago by • 0
5
votes
3
replies
1.1k
views
Linux sort P-values with scientific notation
sort pvalue scientific notation
updated 22 months ago by 10k • written 22 months ago by ★ 8.8k
5
votes
8
replies
659
views
How to get chrM chr1 ...chr22 chrX chrY order in my bam file
snp bam gatk picard sort
updated 23 months ago by ▴ 700 • written 23 months ago by • 0
2
votes
5
replies
828
views
bedtools sort -faidx in CWL
CWL bedtools sort
updated 23 months ago by ▴ 70 • written 2.3 years ago by ▴ 10
1
vote
3
replies
659
views
Pipe pysam.view() output to pysam.sort()
pysam sam alignment python sort
updated 23 months ago by ★ 2.0k • written 23 months ago by ★ 3.4k
3
votes
1
reply
487
views
How can I get this sorted by ascending order? (when the number and character is together)
sort
updated 2.2 years ago by 21k • written 2.2 years ago by • 0
4
votes
14
replies
813
views
How to sort sam file using shell script?
samtools sort sam file Forum
updated 2.3 years ago by 5.0k • written 2.3 years ago by • 0
0
votes
4
replies
1.8k
views
bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the single .bam file?
alignment sort bowtie2 samtools
updated 2.5 years ago by 33k • written 2.5 years ago by ▴ 30
1
vote
2
replies
662
views
Interpro results analysis
column sort
2.6 years ago by ksenia.jravel • 0
3
votes
5
replies
1.1k
views
CD-HIT results without sorting by length
clustering CD-HIT sort length
2.7 years ago by Anand Rao ▴ 420
48
votes
23
replies
19k
views
11 follow
Remove duplicates in fasta file based on ID
fasta sed sort
updated 2.9 years ago by ▴ 60 • written 6.3 years ago by ▴ 160
4
votes
9
replies
1.3k
views
samtools sort: legacy usage
samtools metagenomics genome sort
updated 2.9 years ago by 33k • written 2.9 years ago by ▴ 40
3
votes
1
reply
657
views
Significant Difference of the File Size between csorted and nsorted BAM file
samtools sort compress csort nsort sort
updated 2.9 years ago by 20 • written 3.1 years ago by ★ 8.8k
5
votes
1
reply
2.6k
views
should FASTA files be sorted before indexed with SAMtools?
SAMtools FASTA sort index
updated 3.0 years ago by 14k • written 3.0 years ago by ▴ 70
1
vote
2
replies
4.1k
views
Calculating Average Amino Acid Identity (AAI) using CompareM
AAI ANI CheckM CompareM sort
3.1 years ago by charles.bridges ▴ 70
3
votes
2
replies
1.2k
views
sorting a BAM file
bam sort
updated 3.2 years ago by 7.3k • written 3.2 years ago by ★ 1.1k
2
votes
2
replies
883
views
sort the homo sapiens genes by chromosome with Unix command lines
gene sort
3.3 years ago by Huichen03 ▴ 20
1
vote
4
replies
794
views
Issue while sorting a file
sort trouble inconsistency
updated 3.3 years ago by ▴ 510 • written 3.3 years ago by ▴ 30
4
votes
3
replies
5.9k
views
Sorting with vcftools for tabix gone wrong
vcftools tabix sort vcf index
updated 3.4 years ago by 20 • written 7.0 years ago by ▴ 110
3
votes
6
replies
2.4k
views
Samtools sort error with a bam file
RNA-Seq samtools sort bam
updated 3.5 years ago by 100k • written 3.5 years ago by ▴ 600
2
votes
2
replies
1.6k
views
How to sort an interleaved fastq file by the barcode (BX:Z:) from the header
interleaved fastq barcode sort header
updated 3.5 years ago by 138k • written 3.5 years ago by ▴ 20
8
votes
15
replies
1.7k
views
Sorting my .bam with samtools produces differences in the fastq files generated afterwards
next-gen samtools bam sort fastq
updated 3.5 years ago by 100k • written 3.5 years ago by ▴ 20
2
votes
2
replies
1.0k
views
Sorting file by column, with missing values
glimmer sort awk
3.6 years ago by oars ▴ 180
2
votes
2
replies
4.1k
views
How to specify the sort based on name in samtools sort?
BAM SORT RNA-Seq HTSeq samtools
updated 3.8 years ago by 14k • written 3.8 years ago by • 0
4
votes
9
replies
7.3k
views
Samtools view command, Exec format error while trying to view a human chromosome region
samtools view Exec format error region sort
updated 3.8 years ago by ▴ 960 • written 3.8 years ago by ▴ 30
4
votes
18
replies
1.2k
views
unique list based on multiple column
awk sort
updated 3.9 years ago by ▴ 190 • written 3.9 years ago by ▴ 140
6
votes
9
replies
2.6k
views
featuresCount order sam file?
featuresCount RNA-Seq gtf sort
updated 4.2 years ago by 33k • written 4.2 years ago by ▴ 100
2
votes
3
replies
2.3k
views
samtools sort stuck during merging
samtools sort bamtools next-gen
4.2 years ago by Carlo Yague 6.9k
1
vote
3
replies
1.6k
views
sorting bowtie2 results using samtools sort
bowtie2 samtools sort
4.2 years ago by ggman ▴ 80
38
votes
16
replies
30k
views
7 follow
Efficient And Fastest Way To Sort Large (>100Gb) Bam Files?
sort bam samtools picard
updated 4.3 years ago by ★ 1.6k • written 9.5 years ago by 8.1k
10
votes
2
replies
2.3k
views
Samtools sorting by read names vs. chromosomal coordinates
samtools sort alignment
4.3 years ago by ropolocan ▴ 710
3
votes
5
replies
2.7k
views
Trouble with bedtools groupby - not summarizing by columns
bedtools groupby sort bam
updated 4.4 years ago by ▴ 20 • written 4.8 years ago by ▴ 40
105
votes
24
replies
56k
views
12 follow
Is My Bam File Sorted ?
bam next-gen sequencing sort
updated 4.5 years ago by ▴ 150 • written 10.6 years ago by 138k
1
vote
1
reply
2.2k
views
Is there a way to tell PLINK and VCFtools to sort the samples in a particular order?
PLINK VCFtools sort ped bed
updated 4.7 years ago by 8.4k • written 4.7 years ago by ▴ 400
0
votes
0
replies
1.4k
views
Allele frequencies sorted IGV visualisation
IGV sort AF allele frequency
4.8 years ago by Palani Kannan ▴ 60
5
votes
3
replies
1.9k
views
Sort fastq file by coordinate
fastq sort bam alignment
updated 4.8 years ago by 20 • written 5.0 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Filter criteria for variants based on GBS data
Comment: TCGA dataset normalization
Understanding Imputed Genotypes
C: Cox regression survival analysis - using a panel of genes with TCGA
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C: Scaling data using Pheatmap
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Comment: Weird error from BWA and BOWTIE2 by ATpoint 53k
Do you use a job scheduler such as SLURM, if so please add the submission parameters.
Comment: Use BLAST Command Line Applications on combined FASTA files by Michael Dondrup 49k
Sorry I made a mistake, the name of the parameter `qcovs` not qcov and should be a fraction. Could you try again? For an explanation see ht…
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The problem is with singleton sites (note the number of markers in your window). The solution is to exclude these scaffolds using the exclu…
Comment: Problem with viewing BAM files in IGV by manfi • 0
Samtools view: ![enter image description here][1] Screenshot for 1 line, it seems like the tracks aren't loaded? ![enter image descript…
Comment: RIP-seq : normalize Input with Immunoprecipitated raw counts or not by ATpoint 53k
I have no experience with RIP-seq but usually in something like ChIP-seq one only uses inputs for peak calling as they are globally differe…
Comment: Quick questions about Alevin and AlevinQC by ATpoint 53k
> When I run AlevinQC why the Number of used reads (which Alevin documentation says are reads that are used for quantification) greater tha…
Comment: Problem with viewing BAM files in IGV by Pierre Lindenbaum 138k
> as verified by inspecting the BAM file with samtools view show us a few lines of "samtools view" and show us the screenshot of IGV for …
Comment: compare two vcf files by 순연 • 0
thank u sir , happy Korean Thanksgiving Day 1) how you want to rank those common rs IDs 선생님이 알려주신 코드를 이용해서 두개의 파일에 중복되는 rsID가 있고 또한 여…
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Honestly speaking, your gene list is not "statistically robust" (it's arbitrary since you have no sense of the actual false discovery rate)…
Comment: bedtools getfasta concatenating sequences by Juke34 ★ 6.3k
Ok it is because the first command create gene features only and the second remove gene feature if they do not have any sub-feature like mR…
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yes, that is very possible indeed. however, running blastx on the 'raw' genomic is somewhat less intuitive to interpret. If you have annot…
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Hi, could you please reformat this post using the code `10101` option to highlight code and data?
Comment: desEQ2 eRROR by Nai • 0
res_ddsDE_new has 36,000 rows. When I am using subset(res_ddsDE_new, padj < 0.05 & abs(log2FoldChange) > 1) res_ddsDE_new baseMean log2Fo…
Comment: TCGA dataset normalization by ruby4bioinfo • 0
Thanks Kevin, i got following output str(countData) 'data.frame': 60488 obs. of 183 variables: $ Ensembl_ID : chr "ENSG00000000003…
Comment: Why there are same name with different value in my microarray result? by Aki • 0
Thank you JC! Do you know how to combine these spots as one miRNA? Or do we treat them differently?
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