Biostar

430 results • Page 2 of 9

and find fastq.gz files inside a folder, I tried gunzip -c filename.fastq.gz | head, I get "not in gzip format" error. I tried file filename.fastq.gz, it says "data" (not gzip compressed data as I would expect). When I just double

RNA-Seq

updated 6.6 years ago • S0phia

and their original file types look like this: File: MG430_L4_2.fq.gz, Type: application/x-gzip File: MG431_L4_1.fq.gz, Type: application/x-gzip File:MG431_L4_2.fq.gz, Type: application/x-gzip I ran fastqc, trimmomatic

ASCII fastq text

updated 8 months ago • emi-smiley

it also does not accept bz2 files but then I tried - bzcat input.fastq.bz2 | fastx_trimmer -l 36 -i - | gzip > trimmed.fastq.gz The reason I have used gzip (or may be pigz for making it more fast) here because my next step is mapping...gz files. The above code works but for each file it is taking around 30 minutes. If I don't use gzip in above code then it takes about 22 minutes for ea…

fastq trimming

updated 11.8 years ago • Vikas Bansal

Masking low-complexity regions of downloaded library... done. Downloading plasmid files from FTP... gzip: plasmid.6.1.genomic.fna.gz: invalid compressed data--format violated gzip: plasmid.7.1.genomic.fna.gz: invalid...compressed data--format violated gzip: plasmid.8.1.genomic.fna.gz: invalid compressed data--format violated gzip: plasmid.9.1.genomic.fna.gz: inv…

kraken2 plasmid format violated

updated 3.2 years ago • nathaliaoliveira

Error: could not open writer pipe gzip -cf - < /home/orf8/Desktop/mirna/nc/tmp/left_kept_reads.m2g_um_seg508.fq.z

tophat2

updated 6.4 years ago • priteshrhsabara

in concatenation (.) or string at mapAndGc.pl line 78, <gen1> line 8438174. Can't open output file. gzip: /.gc: No such file or directory gzip: /.map: No such file or directory Kindly tell me how to resolved it , Thanks :(( </gen1></gen1

readDepth non-human-genome

updated 10 months ago • misbahabas

lines in the files with the help of zcat. zcat chr22-filtered.dose.vcf.gz | wc -l Output: gzip: chr22-filtered.dose.vcf.gz: decompression OK, trailing garbage ignored 19 And if I try to unzip the file, I get a similar...message about trailing garbage. gzip: test22.vcf.gz: decompression OK, trailing garbage ignored The file is too large to have only 20 lines, a…

vcf gzip gz plink

updated 12 months ago • pwjeffries

throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134 gzip: stdout: Broken pipe gzip: stdout: Broken pipe Segmentation fault (core dumped) ``` I have 2 Tb free space on the server. What is

hisat2 alignment sam bam

updated 15 months ago • Ngrin

do "cat" on them, but is there any faster way? can I use gzcat file1.fastq.gz file2.fastq.gz | gzip > merged.fastq.gz

merge fastq

updated 10.6 years ago • newDNASeqer

place it into document directory of HTTPD server in your computer and uncompress it by > gzip -d viroblast.tar.gz > tar -xvpf viroblast.tar > It is important to have the parameter "p" in tar options. It will preserve...writeable and executable permissions for everyone (777). Everytime I enter that first command – `gzip -d viroblast.tar.gz` – into terminal, I …

viroblast blast SQL PHP sequence

updated 7.8 years ago • cllezark

everyone i am trying to unzip a file with the command " gunzip file_name.gz " and getting this error. gzip: invalid compressed data--crc error invalid compressed data--length error How can i unzip my files

genome sequencing sequence

updated 4.5 years ago • microbez.uaf

sample (cat) and when I ran Fastq it gives me error that file is truncated. when I looked at tail gzip: ABC_10_XXX_ACCTCA_L001_R2_merged.fastq.gz: unexpected end of file + 0<0

RNA-Seq error fastq

updated 7.9 years ago • rob.costa1234

PE reads at once using minimap2? I tried something like this: minimap2 -x sr *_1.fq.gz *_2.fq.gz | gzip > prefix.paf.gz But it did not work. Thanks, Raz

alignment sequencing minimap2

updated 4.9 years ago • barvazduck

Hi everyone! I'm a newbie in genomic data analysis, that’s why I’m asking for some help in things that might be easy in fact. I have a zipped vcf-file, which contains human chromosome 20 sequences for 269 individuals. I want to filter out singletons and doubletons for subsequent analysis. I use vcftools v0.1.15 installed on a server. Here is what I do: vcftools --gzvcf chr20_269ind.vcf.gz -…

snp software error next-gen

updated 7.4 years ago • vasilipankratov

a few compression tools for fastq files. So far on my list I have the following: 1. dsrc 2. lrzip 3. gzip 4. bgzf Anyone have any good/poor experience with any of the above, or other options? I'll be trying them all plotting compression...considered. Indexing and RAM usage are not of concern. **EDIT Oct 28, 2015**: We have tested lrzip, gzip, dsrc, bzip2, and others and found that by far dsr…

fastq compression

updated 19 months ago • Richard

I see that one of the input files is missing. ``` bwa mem -a -t24 -S -P -k63 myassembly_k63-8.fa \ |gzip >../long_contigs.fasta-8.sam.gz bwa mem -a -t$j -S -P -k$l $(name)-8.fa $(strip $($*)) \ |gzip >$@ ``` As you can see, the following fragment of the code

abyss assembly

updated 19 months ago • wstfljs

at uk.ac.babraham.FastQC.Sequence.FastQFile. I used the solution for the previous posts.I get this: gzip: invalid compressed data--format violated Is my data originally damaged

RNA-Seq software error fastqc

updated 4.7 years ago • 2899135311

master/database/jobs_directory/000/24/tool_script.sh: line 9: fastx_clipper: command not found gzip: stdout: Broken pipe

Galaxy fastxtools

updated 8.0 years ago • anjyou.80

This code work perfectly def read_vcf(file_path): with open(file_path, 'r') as f: lines = [l for l in f if not l.startswith('##')] return pd.read_csv( io.StringIO(''.join(lines)), dtype={'#CHROM': str, 'POS': int, 'ID': str, 'REF': str, 'ALT': str, 'QUAL': str, 'FILTER': str, 'INFO': str}, …

vcf gzip pandas

updated 2.2 years ago • ManuelDB

like this: ```py import os, sys, subprocess, argparse, random, transposer, numpy, csv, scipy, gzip ``` I installed "transposer" on my local/mac by: ``` python3 -m pip install transposer ``` BUT, I got this error: ``` Traceback (most recent...call last): import os, sys, subprocess, argparse, random, transposer, numpy, csv, scipy, gzip File "/opt/homebrew/lib/python3.10/site-packages/transpos…

python conda transposer

updated 17 months ago • Razi

read it as a vcf file. found some code to do it in python : #!/usr/bin/env python3 import gzip ifile = gzip.GzipFile("gnomad.genomes.r2.1.1.sites.2.vcf.bgz") ofile = open("truncated.vcf", "wb") LINES_TO_EXTRACT = 100000...ifile.readline()) ifile.close() ofile.close() i tried it on my data : import gzip ifile = gzip.GzipFile("gnomad.exomes.r2.1.1.sites.…

vcf gnomad bgz

updated 17 months ago • Eliza

Does fastx_toolkit accept *fastq.gz file as input file? Or does it have to be fastq/a file? I get the following error message when i try fastx_clipper -Q33 -z -a GATC -i my.fastq.gz -o my_adapRem.fastq fastx_clipper: input file (my.fastq.gz) has unknown file format (not FASTA or FASTQ), first character = (31) is this because of zipped input data or am i missing something else?

fastx fastq

updated 10.6 years ago • roll

figured out tabix part with `pysam.tabix_index` but I don't know how to create `gz` file. I've tried `gzip` module from Python itself but `pysam.tabix_index` was unhappy about it. Does anyone know how to do it

python bgzip

updated 2.1 years ago • magnolia

in the below command: nohup /mnt//sratoolkit.2.8.2-1-centos_linux64/bin/fastq-dump --split-3 --gzip SRR1785709 SRR1785715 SRR1785721 SRR1785728 SRR1785734 SRR1785742 SRR1785744 >nohup.out &amp

RNA-Seq

updated 5.7 years ago • Bioinfonext

Dear All I have tried to merge two vcf files by using vcf-sort, gzip, tablix followed by vcf-merge. The resultant merged file contains variants on chromosome 1 only. Any comment/help would

next-gen sequencing SNP genome

updated 3.6 years ago • mkamranazim

fastq.gz files were formed by SRA toolkit using fastq-dump. fastq-dump -I --split-files --gzip When I try to run the two files for analysis by fastp I am unable to specify the two paired end files inside my shell script..._trimmed.fastq.gz -O ${file2}_trimmed.fastq.gz done ``` but it gives an error: Error to read gzip file ............... the file doesn't exist. I don't know where …

shell fastp RNA-Seq bash

updated 4 months ago • Mithil Gaikwad

command. But there are two fastq files for sample, R1 and R2. I used this command. $ fastq-dump --gzip --split-files SRR5945694 Did I use wrong command? Thank you in advance

RNA-Seq single-cell

updated 3.3 years ago • dahun73

know what's happening here? How can I get my phased file? Here's my code running beagle and using gzip: java -Xss5m -Xmx100g -jar /Users/xupeiyu/Downloads/beagle.28Jun21.220.jar gt=sex727_vcf.vcf out=phased_2 gzip -c phased_2.vcf.gz

beagle vcf

updated 2.6 years ago • Xu

downloading 1000 genomes phase 3 vcf files from http://www.internationalgenome.org and have used gzip to decompress them. I have used two different computers to do this and on one I get a substantially larger uncompressed...All three of the .vcf.gz files were around 1gb each before unzipping. I have the same version of .gzip on both systems (though surely that cannot cause such a diverse range of…

vcf

updated 6.9 years ago • spiral01

Masking low-complexity regions of downloaded library... done. Downloading plasmid files from FTP...gzip: abort: corrupted input -- invalid deflate data: plasmid.11.1.genomic.fna.gz gzip: abort: corrupted input -- invalid deflate...data: plasmid.3.1.genomic.fna.gz gzip: abort: corrupted input -- invalid deflate data: plasmid.5.1.genomic.fna.gz gzip: abort: corrupted input -- invali…

databaase kraken2 metagenome

updated 2.3 years ago • mathavanbioinfo

compound structures of PubChem Database. I have download SDF file for PubChem, but it is 45G after gzip. If I convert all SDF file to SMILES, that won't be easy... Is there any way to retrieve all SMILES for the whole PubChem? Thanks

compound pubchem

updated 19 months ago • ajingnk

be: gunzip -c SampleName_Barcode_Lane_R1_001.fastq.gz | \ fastq_illumina_filter-Linux-x86_64 -vvN |gzip -9 \ >SampleName_Barcode_Lane_R1_001_filtered.fastq.gz Now using GNU Parallel, here is what I thought would work...gunzip -c SampleName_Barcode_Lane_R1_00{1}.fastq.gz | \ fastq_illumina_filter-Linux-x86_64 -vvN |gzip -9 \ >SampleName_Barcode_Lane_R1_00{1}_filtered.fast…

parallel fastq illumina

updated 12.5 years ago • jvijai

files after use fastq-dump to extract fastq files from sra files. command :fastq-dump --split-3 --gzip SRR4242282.sra I have no idea with this result, I haven't met this before. Any suggestion would be appreciated

sra fastq-dump fastq

updated 5.6 years ago • fanglujing

xargs cat > CG1-1_1.fq.gz`, HOWEVER, when I `gunzip` the concatenated .fastq.gz , it showed gzip: 80OF_01.fq.gz: invalid compressed data--crc error gzip: 80OF_01.fq.gz: invalid compressed data--length error which suggested

RNA-seq

updated 22 months ago • slin023

import gzip input_file = open("example.bed","rb")#compress existing file data = input_file.read() with gzip.open("example.bed.gz", "wb") as...delimiter='\t',header=1 ) df.to_csv('exampleziptotxt.bed', index=False) import gzip import os file_name = "exampleziptotxt.bed" out_file_root = "example_by_chrom" file_handle_dict = {} with open(file_name

bed python gzip

updated 3.6 years ago • dk0319

apos; Content type 'application/x-gzip' length 515201 bytes (503 KB) ================================================== downloaded 503 KB probando la URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.3.tar.gz...apos; Content type 'application/x-gzip' length 3058840 bytes (2.9 MB) ================================================== downloaded 2.9…

RNA-Seq

updated 3.2 years ago • acs

I have been running the following command to convert SRA files: fastq-dump -F --gzip --readids --split-files And I want to transition to fasterq-dump. Which would be the equivalent command? I think it is(given

fasterq-dump

updated 3.5 years ago • requiem_data

the command I am passing through: `salmon quant -i <directory containing="" index=""> -l A -1 <(gzip <path .fastq.gz="" file="" to="">) -2 <(gzip <path .fastq.gz="" file="" to="">) --validateMappings -o <output directory="">` Here is what `directory containing

salmon RNAseq

updated 2.8 years ago • saipra003

error when I call the commands from R or Python: `the file is not BGZF compressed` The files are gzip-compressed variants. Why it's working only through the command line

bcftools

updated 10 months ago • Mali

chr22_snpeEff_summary.html >chr22_joint_genotyped.ann.vcf.gz ``` The output VCF is not in `gzip` format. Is there way to output the snpeff output in `.vcf.gz` format

snpeff

updated 10 months ago • ttom

fastq files individually. I am using NanoFilt for trimming. All Fastq files are in the directory(not gzip format). How can I write a loop or command line for trimming all fastq files individually? I am using Linux Ubuntu 21.04

Trimming Nanopore Fastq Rna-Seq

updated 3.0 years ago • Çağatay

gzipped). I tested it on a few gzipped fastq files. Although it worked well with almost all test gzip files, it stopped early on one test file and I could not track down why. Therefor inputting gzip files is still experimental

DEL NGS CRISPRseq

updated 2.6 years ago • coffeyrt

Content type 'application/x-gzip' length 1010422 bytes (986 KB) ================================================== downloaded 986 KB trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/SummarizedExperiment_1.6.5.tar.gz...Content type 'application/x-gzip' length 980552 bytes (957 KB) ================================================== downloaded 957 KB tryin…

DESeq2 R Rstudio

updated 6.5 years ago • grant.hovhannisyan

code in conda enviroment: nohup cat list.txt | parallel --jobs 10 fastq-dump {} --split-3 --gzip -O ./ > log.txt 2>&1 & After I logging out from the terminal, the log.txt shows : parallel: SIGHUP received. No new jobs

parallel nohup

updated 11 months ago • gavin

denisovan/chr"$i"_mq25_mapab100.vcf.gz --bed bed/chr"$i"_mask.bed --recode --keep-INFO-all --stdout | gzip -c > filtered/denisovan.filtered."$i".vcf.gz; done This is proving extremely slow. Is there any tool that is much quicker

SNP

updated 6.5 years ago • spiral01

home/aclab/find_circ/unmapped2anchors.py /home/aclab/CircRNA/find_circ/unmapped/unmapped.bam | gzip >/home/aclab/CircRNA/find_circ/unmapped/anchors_unmapped.fastq.gz I got this error------- File "/home/aclab/find_circ/unmapped2anchors.py

RNA-Seq

updated 4.8 years ago • harry

be modified to concatenate all VCF files from a directory. vcf-concat A.vcf.gz B.vcf.gz C.vcf.gz | gzip -c > out.vcf.gz instead of A.vcf.gz, B.vcf.gz I would like all vcf.gz from my directory concatenated knowing they are

vcf

updated 10.3 years ago • win

way to do that using VCFtools? Code I used: vcf-concat File1.vcf.gz File2.vcf.gz File3.vcf.gz | gzip -c > Merged.vcf.gz Many thanks! Parvathi

NGS VCF Strelka2

updated 3.1 years ago • parvathi.sudha

alignment for multiple files, but I suddenly get the error messages "salmon: command not found" and "gzip: command not found". The command I use in terminal (single files) is: salmon quant -i human_index --libType A -r /Rprojects/Sweet_et_al...Rprojects/Sweet_et_al/fastq/SRR7426${i}.fastq -o ${PATH}/Rprojects/Sweet_et_al/quant/SRR7426${i} gzip ${PATH}/Rprojects/Sweet_et_al/quant/SRR74…

alignment RNA-Seq

updated 3.5 years ago • martijnhoes5

a library (reads in paired-end) using this: seqtk sample -s100 ./SRR2937435_1.fastq.gz 10000 | gzip > sub1.fastq.gz seqtk sample -s100 ./SRR2937435_2.fastq.gz 10000 | gzip > sub2.fastq.gz The sub1_val_1.fq.gz file

fastq FASTQC Fastqc

updated 7.1 years ago • beausoleilmo

430 results • Page 2 of 9

Recent Votes

Convert vcf files with phased genotypes to standard haplotype format

A: Convert vcf files with phased genotypes to standard haplotype format

How to extract haplotype data from phased bcf files

Answer: RNA-seq data for deep learning classification

Answer: Analysis of intronic reads included scRNA-seq data

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