Biostar

430 results • Page 3 of 9

immediately to stdout? Right now I have to wait the 1 hour or so it takes for bcl2fastq to make a gzip file that I can unzip. I'd like to immediately pipe this data to stdout if possible. I don't see a command line option in the

bcl2fastq illumina next-gen

updated 3.3 years ago • b10hazard

in the folder. The following is an example of what's happening: tar -xvzf rlsim-latest_amd64.tar.gz gzip: stdin: unexpected end of file tar: Child returned status 1 tar: Error exit delayed from previous errors

updated 10.2 years ago • thejustpark

getting the reference genome: (base) [caiqi@midway2-login2 genome_fa]$ gunzip ref.GRCh38.fa.gz gzip: ref.GRCh38.fa.gz: unexpected end of file (base) [caiqi@midway2-login2 genome_fa]$ zcat ref.GRCh38.fa.gz > ref.GRCh38.fa...gzip: ref.GRCh38.fa.gz: unexpected end of file So I tried to get the reference genome from the iGenome website to do the STAR

sequencing RNA-Seq

updated 4.1 years ago • Kai_Qi

F "upload=@/home/auroshis/fastq_files/SRR16124173.fastq.gz" -F "compression=gzip" "https://api.mg-rast.org/inbox" But I am getting this error - curl: (55) OpenSSL SSL_write: Broken pipe, errno 32 Can anyone help

auroshis

updated 2.2 years ago • Auroshis

to get the barcode file of SRR7191904. Thanks in advance for any help! Best, Yue fastq-dump --gzip --split-files SRR7191904.sra bin$ head -n 10 SRR7191904_1.fastq @SRR7191904.1 1 length=27 GATCGNGGTCCTGCTTCGCCTATGTCT

RNA-Seq

updated 4.4 years ago • yueli7

mpileup -C50 -uf reference individual | \ bcftools call -c | vcfutils.pl vcf2fq -d 10 -D 100 | \ gzip > out.fastq fq2psmcfa -q20 out.fastq > psmc.fa I would like to use a bed file with repeat and gene coordinates to mask

fastq bed psmc

updated 3.8 years ago • thjnant

zcat final_all_merged.vcf.gz | awk 'length($5) + length($(4)) < 4' >> only_short_indels.vcf gzip only_short_indels.vcf I believe Pierre's solution will also work, just too lazy to install additional toolkit on cluster...one liner zcat final_all_merged.vcf.gz | awk '($1 ~ /^#/ || length($5) + length($(4)) < 4)' | gzip > only_short_indels.vcf.gz

VCF

updated 2.7 years ago • German.M.Demidov

Hi, I am using script remove_mapping_reads.py from EBV portal https://ebv.wistar.upenn.edu/tools.html. In running the script there is an error: Traceback (most recent call last): File "remove_mapping_reads.py", line 4, in import sys, os, bisect, time, pysam, aln, gzip ModuleNotFoundError: No module named 'aln' I googled how to install python module 'aln' but seems could not find it. Ma…

python module ebv

updated 6.5 years ago • teresayahu

them with both winrar and the command unrar obtaining this: file control_1.bam control_1.bam: gzip compressed data, extra field when I try to see the file this message comes up head control_1.bam head: error writing 'standard

alignment

updated 4.3 years ago • jomagrax

a gene in the following way: > bwa index ref.fasta > bwa mem ref.fasta sample5-21.fq | gzip -3 > sample5-21.sam.gz > splitsam.sh sample5-21.sam.gz forward.sam.gz reverse.sam.gz Total reads: 1792444 Plus

gene alignment RNA-Seq

updated 5.5 years ago • Ric

Edit: I'm writing python myself. My python script goes like: #!/usr/bin/python import os, sys,re,gzip path = "/home/xxxx/Downloads" for file in os.listdir(path): if re.match('.*\.recal.fastq.gz', file): text = gzip.open(file,'r').read() word_list...2] No such file or directory: 'ERR001274_1.recal.fastq.gz' I think there's sth wrong with the gzip, and also why can't I open ERR00127…

python

updated 12.9 years ago • Bioscientist

tv Feature - Spreadsheet-like view for delimited data - Vim-like key binding - Support for gzip compressed file - Automatically identify tsv and csv format(Experimental) ![enter image description here][1] [1]: https://github.com

viewer software

updated 10 months ago • codechenx

referenced above. I've found an open source tool called DSRC (~37% additional compression over gzip), but it's nowhere near as good as Genozip. DSRC: https://github.com/refresh-bio/DSRC It appears that Genozip is the best compression

GZIP FASTQ BAM

updated 2.3 years ago • kstangline

to manual i have tried with "tar -zxf SOAPdenovo2-master.zip" command line. Then it was showing 'gzip: stdin has more than one entry--rest ignored tar: Child returned status 2 tar: Error is not recoverable: exiting now'. Can someone

software error

updated 3.5 years ago • kishorssf91

I've had some difficulties implementing this in pipelines because it randomly fails sometimes. Are there any other programs that can be used in its stead?

fastq genomics rnaseq

updated 2.3 years ago • O.rka

download a few RNAseq data from NCBI using SRA toolkit with the following command: fastq-dump --gzip SRR924395 and I'm getting the following error: fastq-dump.2.6.3 err: function unsupported while opening file within...that I can download one specific RNAseq data (SRR924399) with the following command: fastq-dump --gzip SRR924399 but for all the other data that I tried, I got t…

fastq-dump RNA-Seq sratoolkit

updated 10 months ago • BCArg

these commands: for positive strand, `bedtools coverage -a my_region.bed -b file.bam -bed -d -s | gzip > coverage_positive.tsv.gz` and for negative strand `bedtools coverage -a my_region.bed -b file.bam -bed -d -S | gzip > coverage_negative.tsv.gz

bam bed coverage

updated 5.2 years ago • MAPK

I tried downloading it with fastq-dump --outdir /N/p/lab.mis/elliot/bulk/raw_ext_JEM/raw/ --gzip --split-files SRR6826132 however this only resulted in single fastq file, SRR6826132_1.fastq.gz is there way I can make

rnaseq geo

updated 18 months ago • simplitia

However command bcftools mpileup -R regions.tab -f genome.fa aln.bam | tee /dev/tty | gzip > output.vcf.gz stalls and no output is produced. Running the same command with a three column bed file like below instead

bcftools

updated 2.3 years ago • mb

1a_H7JMMBBXX_L5_1.fq.gz -f2 NISAR2_CKDL200148448-1a_H7JMMBBXX_L6_1.fq.gz -i barcode.txt -m 0 -al no -gzip true -o 01_Nisar_Demultiplexing then we got following error GBS demultiplexing ended with Major Errors Can anyone

software error SNP gene next-gen genome

updated 4.2 years ago • harshraje19

dump tool. Here is the line of code we've learnt in class to do so: fastq-dump --split-files --gzip --skip-technical --readids --read-filter pass --clip SRR12737830 I was wondering if the "--split-files" was very useful given the

RNA-Seq

updated 3.6 years ago • eva.lucarelli

Today I consider the raw data to be the demultiplexed fastq files in gzip format that come off the sequencer. I believe many years ago there was a different output of data from sequencers. I have

sequencing

updated 5.4 years ago • Tawny

Content type 'application/x-gzip' length 1432307 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/geneplotter_1.58.0.tar.gz...Content type 'application/x-gzip' length 1428691 bytes (1.4 MB) ================================================== downloaded 1.4 MB tryi…

R rna-seq gene

updated 4.4 years ago • enginbozaba

Dear community, I am trying to convert BAM to FASTQ because the archived dataset is aligned to the older version of the reference genome. I need to realign to the new version. SRA is not available (I know, devastating experience). I tried two different approaches and both of them show errors: Approach 1. Merge all BAM files into one (each BAM file represents alignment per chromosome). The err…

samtools

updated 11 months ago • Qboy

Hey everyone, I am having some issues updating some packages. I am using `Bioconductor 3.18` and sometimes, when I want to update my packages using `BiocManager::install()` (or, if I install a specific package), I am asked, if I want to update some packages. So far so normal and I mostly select all then. Most of the packages are updated, but some simply aren't. I don't get a warning or error for…

Bioconductor

updated 3 months ago • gernophil

above command I prepared mpileup files through samtools command: **> samtools mpileup file.bam | gzip -c > file.mp.gz** However I am not sure how to make this refpanel-phased vcf file for wheat. Looking forward to your valuable

loimpute imputation phasing

updated 4 months ago • analyst

efetch -format runinfo | cut -d ',' -f 1 | grep SRR | xargs -n 1 -P 4 fastq-dump --split-3 --gzip --skip-technical --readids -W --read-filter pass After 12 hours, it's still downloading (5152 items thus far). Did I use the wrong

sra

updated 2.1 years ago • melissachua90

vcftools --gzvcf xxx --remove-indels --maf 0.05 --max-missing 0.85 --minQ 30 --recode --stdout | gzip -c > xxx.filtered.vcf.gz

SNP vcftools max missing genome

updated 3.4 years ago • truebeliever24

Hi all, I recently downloaded some gzipped fastq files (fq.gz) directly to my local machine from an online repository (dropbox) and due to my settings in Safari (to open safe files) my computer tried to unzip these files and they ended up truncated (each file should have been ~200MB but they all ended up as 65KB but still "looked" like a fasta file in the sense that the first several thousand …

gzip fastq

updated 2.2 years ago • eb13

opening: "/test/Batch1_S1_L006_R2_001.fastq.gz" got recs: 28810048 got recs: 48304343 error: corrupt gzip stream does not have a matching checksum caused by: corrupt gzip stream does not have a matching checksum ------------ If you believe

cellranger

updated 11 months ago • tien

index bwa index $genome_file #BWA mapping bwa mem -t 8 $genome_file $fastq_file_R1 $fastq_file_R2 | gzip -3 > P_S1_L001_aln-pe.sam_inverted.gz bwa mem -t 8 $genome_file $fastq_file_R3 $fastq_file_R4 | gzip -3 > V_S1_L001_aln

paralogs BWA RNA-Seq MAPQ

updated 2.3 years ago • biotech

prev_header=$0} END {print header; print max_seq; getline; getline; print; getline; print}' | gzip > reads_max_length.fastq.gz Also, when I align with minimap2, I don't get any results. Maybe I did something wrong? Thanks

fastq

updated 10 weeks ago • marco.barr

but receive an error: ```r > test <- sequenza.extract(seqz.data) Error in pipe(paste("gzip -d -c", file, "| cut -f 1,6,10")) : invalid 'description' argument ``` Can anyone explain this to me in a bit further detail? Is there just something

sequenza CNV

updated 20 months ago • zhaolianhe1992

cut -d ',' -f 1 | grep SRR | xargs -n 1 ./../sratoolkit.3.0.0-ubuntu64/bin/fastq-dump --split-3 --gzip --skip-technical --readids -W --read-filter pass However, the runs that were downloaded were not split into two files. For each

paired-end sra

updated 2.1 years ago • melissachua90

these for each chromosome and then concatenated them. These files are in a format that gunzip/gzip -d wont recognize. I tried using this file unzipped in bedtools intersect but it wasn't reconized. Many thanks

updated 3.7 years ago • GPR

the result only has one file. Thanks in advance for any help! Best, Yue /bin$ fastq-dump --gzip --split-3 --defline-qual '+' --defline-seq '@\$ac-\$si/\$ri' SRR6956073.sra Read 161274652 spots for SRR6956073.sra Written 161274652

RNA-Seq

updated 4.4 years ago • yueli7

paired.fq from this command: `htscmd bamshuf -Ou input.bam tmp-prefix | htscmd bam2fq -s se.fq.gz - | gzip > pe.fq.gz` ([Source][2]) I got only 41k pairs. After deinterleaving output of this command `htscmd bamshuf -uOn 128 aln_reads.bam...tmp | htscmd bam2fq -a - | gzip > interleaved_reads.fq.gz` ([Source][3]), I got 232.7k reads for one end and 214.4k reads for the other end. Is…

Fastq Bam2Fastq Tophat BAM HTSlib

updated 2.4 years ago • trakhtenberg

100% INFO Downloaded file ref_GRCh37.p13_top_level.gff3.gz looks like a valid gzip'ed file INFO Downloading https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105...100% INFO Downloaded file rna.fa.gz looks like a valid gzip'ed file INFO Downloading http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz [========…

jannovar

updated 9 months ago • curious

SRR | xargs fastq-dump -X 10000 --skip-technical --readids --read-filter pass -dumpbase --split-3 --gzip The error that appears for me: 2022-12-24T17:30:25 fastq-dump.2.8.0 err: param empty while validating argument list - expected

SRATools

updated 11 months ago • usef

Documents/Kraken_out/A1_report --use-mpa-style /home/rakesh/Documents/Kraken_out/A1_mpa_style_rep --gzip-compressed Kindly help me resolve the issue. Thanks

metagenomics kraken2

updated 23 months ago • serene.s

geo/series/GSE76nnn/GSE76124/matrix/GSE76124_series_matrix.txt.gz' Content type 'application/x-gzip' length 58695125 bytes (56.0 MB) ================================================== downloaded 56.0 MB Error: The size of the connection buffer (131072) was not large enough

data studio R import GEOquery

updated 2.5 years ago • ponmalar1120

while read line;do echo "Line No. $n : $line" fastq-dump --split-files --gzip $line -O /data/scratch/anna9230/Khrameeva_data /snRNA_data/ done < SRR_Acc_List_snRNA.txt after the first file which

SRA

updated 3.9 years ago • annaA

I was running Bloocoo-1.0.4 (part of GATB) on two gzip'd fastq files. The documentation says that I can provide the two files in a comma separate list like "read1.fq.gz

GATB

updated 9.3 years ago • lh3

URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/Seurat_3.2.2.tgz' Content type 'application/x-gzip' length 3541892 bytes (3.4 MB) ================================================== downloaded 3.4 MB **library(dplyr)** **library(Seurat)** macOS Catalina (10.15.1) Seurat_3.2.2 RStudio

rna-seq R

updated 3.6 years ago • reza.mirzaei

Hello, I downloaded GSE62772 with getGEO() function of GEOquery package. I tried to extract expression data matrix but I have logical result and an empty matrix. My codes are: > gse62772 <- getGEO("GSE62772") https://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62772/matrix/ OK Found 2 file(s) GSE62772-GPL11154_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/seri…

geoquery bioconductor gse

updated 6.5 years ago • hkarakurt

Dear all, I have a fastq.gz file that has more than 100 million reads. My aim is to divide this fastq file into three separate fastq files, ensuring that all reads from the original fastq file are distributed and unique in the newly created fastq files. I tried using ```fastqsplitter``` as below but I get the mentioned error: ``` fastqsplitter -i 10_S10_R1_001.fastq.gz -o group4_sample10_R…

fastq sequencing rna-seq

updated 12 months ago • Apex92

Hi, I want to merge multiple .fastq.gz files (forward/Reverse), and using following command: zcat dir1/ETH002281_ACAGTG_L00*_R1_00*.fastq.gz dir2/ETH002281_ACAGTG_L00*_R1_00*.fastq.gz dir3/ETH002281_ACAGTG_L003_R1_001.fastq.gz | gzip > dir4/ETH002281_ACAGTG_Lall_R1.gz Although it run fine but it takes huge time as I am able to run it on single node, I...fastq.gz dir2/ETH002281_ACAGT…

Assembly next-gen-sequencing

updated 20 months ago • ravi.uhdnis

R2 files to one file for each sample (folder). I can't see an automated version rather than just gzip each subfolder in turn but likely there is a bash way which completely missing? i.e. within folder "plateK" Sample1_folder

bash

updated 19 months ago • rob234king

a lot! I used this command: trim_galore -q 20 --phred33 --length 20 ERR791838.fastq.gz --gzip -o ./cleandata/trim_galoredata/ But it didn't works. And I got an error File seems to be in SOLiD colorspace format which is

SOLiD adapters Trimming

updated 2.9 years ago • kimmitzka

dumped it to fastq. ~/tools/sratoolkit.2.4.2-centos_linux64/bin/fastq-dump -I --split-files --gzip SRR1514952/SRR1514952.sra BWA mem is throwing and error when I'm aligning the mate pairs: ``` [mem_sam_pe] paired reads have

paired sra fastq bwa mem

updated 2.2 years ago • Zev.Kronenberg

430 results • Page 3 of 9

Recent Votes

A: Peaks And Nearby Genes

Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version

Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

Answer: TFs and Gene databases

A: Is there a software that can compare phylogenetic trees to each othe (face to fa

Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset

Recent Locations • All