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12,241 results • Page 2 of 245

different from each other in terms of read length, coverage, library type etc. Now I have ~30 fasta files, each derived from a single data set. Next, I'd like to merge them in order to get a single, unified transcripts set. I...that I have de-novo assembled. Here are my questions: 1) Do you know of a tool that can do the merging I'm looking for? When I say merge, I mean do it in a smart way,…

Assembly RNA-Seq

updated 5.8 years ago • liorglic

I am trying to asembly several fasta files following the same steps but one of them I can not. The steps that I followed are: # I removed no mapped reads of my fastq...PV003_1_trim.fq PV003_2_trim.fq # I combined both parts of my fastq files and I converted it in fasta file: fq2fa --merge PV003_1_trim.fq_pairs_R1.fastq PV003_2_trim.fq_pairs_R2.fastq PV003_cmv3.fa #after that

assembly ngs

updated 5.0 years ago • apl00028

I have two Seurat objects that were made by merging of samples: object1 <-merge(A, y=B, add.cell.ids=c("A","B")) object2 <-merge(C, y=D, add.cell.ids=c("C","D")) For each object I did all preprocessing...PCA, and clustering. Now I want to merge cluster 1 from object1 and cluster 3 from object2 cluster1<-subset(object1, ident=1) cluster3<-subset(obje…

scRNA-seq Seurat single-cell R RNA-Seq

updated 3.4 years ago • biostarukha

Hi, What does column C (somewhere transcript and exon) represents in merged output gtf file by StringTie? Secondly, I need to extract FASTA sequences for few ids formed by new transcript files...I consider all the corresponding start and end sites? If no, then what to do? Kindly respond. ![Merged GTF file][1] [1]: /media/images/69a192d9-611d-4823-925d-4f9734ba

StringTie GTF merged

updated 22 months ago • Roy.anupama11

with analyzing my ChIP-seq data. I have an IP, input with replica (ChIP1, Input1, ChIP2, Input2). I merged the alignement files (.bam hg19) with bamtools merge, then called peaks. The problem is merging summs the reads at a given...position. Like: So, the final goal is, how to merge the samples as the read numbers averaged not summed at same positions? Regards, Laszlo

bam merge

updated 10.4 years ago • hlsz.laszlo

I have a fasta file of DNA sequences for two different species across a chromosome, e.g. ``` >SpeciesA_gene1 ACTGC..... ``` and ``` >SpeciesB_geneX...I have a fasta file of DNA sequences for two different species across a chromosome, e.g. ``` >SpeciesA_gene1 ACTGC..... ``` and ``` >SpeciesB_geneX TCTGC... ``` and a text file of orthologs ``` SpeciesA SpeciesB g…

fasta clustal

updated 16 months ago • burnsro

seq on mice and I used 3x E. coli tRNA spike-ins. I'm assuming for analysis, I'll have to generate a fasta and GTF file for these spike-ins? If so, how do I do this? Also, I'm assuming this will have to be merged with the mouse fasta and

RNA-Seq spike-in

updated 5.5 years ago • 2405592M

Hi there, I'm not sure about the following: if you use `bcftools merge` to merge *vcf.gz* files does it merge the overlapping variants only or does it also merge variants that are present in

SNP bcftools merging

updated 5.6 years ago • isabel.hostettler.14

some metagenomic samples and I have individually assembled them with Spades. Now I would like to merge the contigs.fasta files from my samples (I want to proceed with mapping and binning using anvi'o). Which is the most appropriate

Assembly Anvi’o fasta

updated 5.3 years ago • anastasia.gs17

Hi, I'm trying to concatenate hundreds of .fasta files into a single, large fasta file containing all of the sequences. I haven't found a specific method to accomplish...this in the forums. I did come across this code from http://zientzilaria.heroku.com/blog/2007/10/29/merging-single-or-multiple-sequence-fasta-files, which I have adapted a bit. Fasta.py contains the following code: class fa…

fasta python

updated 11.8 years ago • charles.bridges

Hi All, I am trying to use vcf-merge. However on my test batch of 6 files, only the first two merge. vcf-merge ${all_gz_vcfs[*]} | bgzip -c > merged.vcf.gz My suspicion...is that since these VCF files came from three different modifications of ANNOVAR, vcf-merge is not working as intended. Would anybody have have insight towards a possible fix or has ran into this problem before

software error

updated 6.8 years ago • zihan98li

Hello I am having an error using the following command line: stringtie --merge -p 8 -G /home/ltr2/Genomes/GTF/hg19.gtf -o onwork/hisat2_test/gtf/stringtie_marged.gtf onwork/hisat2_test/margelist.txt...bam files has been sorted and indexed with samtools (so they are sorted) and hg19-fasta and hg19.gtf have been download from ucsc web page magelist has one file per line with its full path …

RNA-Seq stringtie

updated 5.6 years ago • paumarc

Hi to everyone, I got some environmental metagenomes. I would like to merge the pair reads (forward and reverse), which are already denoised, and not anymore in fastq format but in fasta. Looking around...as input fastq reads. There are some tools like reformat of BBmap, which could allow me to reformat fasta to fastq cheating on the quality. Thus, what I was thinking to do is: reformat al…

pear merging illuminareads

updated 2.8 years ago • Lapsus

Hi All, I want to merge 38 vcf files with bcftools merge: bcftools merge --force-samples -l input.txt -Oz -o LungBrain.vcf.gz However, bcftools...report error: Incorrect number of F1R2 fields (2) at chr12:29486505, cannot merge. I checked this variant and found: chr12 29486505 . CAG C,CTAG 16.87 . GT 0/0 0/0 ./. 0/2 Any suggestion? Thanks

SNP vcftools merge F1R2

updated 4.8 years ago • Shicheng Guo

Hi all, I have several maize GBS raw data (less than 10) from the same family. I wish to merge these individual sequence into one ., meanwhile fix and patch the mistakes of SNPs. For example: sample 1: NNNNN TTCGG TNNGC...sample 2: NNNNN TTCCC TNNGC sample 3: NNANN NTCGG TNNGC merge and fix to: NNNNN TTCGG TCCGC Once the SNP shows up in 2 samples then considered as a real SNP otherwise no ch…

GBS SNP maize

updated 8.0 years ago • anjun.ma

Hi, I want to merge list of bam files (after I already sorted them previously) using samtools merge. I have a list of bam files that I want to...sent from python to the following command in bash: ${samtools} merge - ${bam_source}/${sample_name}.merged.bam Will samtools work with list from python as input? is the above scrips in general

python bash samtools

updated 6.1 years ago • Bella_p

Hello all, Hope you're well. I started a PhD in Jan this year and frankly I am struggling. I'm coming into the second week of trying to figure out how to attempt this problem and it's honestly starting to get to me a bit - the current task I'm working on is not my main project and every day I don't make progress is a delay on my actual project. So! A bit worried to say the least (!) Here is the…

GenBank Fasta Linux Python BLAST

updated 2.6 years ago • Leah

Hello! I am trying to merge files in plink, I used the following command:- ./plink --file data1 --merge data2.ped data2.map --noweb --recode --out merged. In my...out file "merged file", some chromosomes are missing, which command can I use to merge files without losing data? Thank you in advance

SNP plink gwas

updated 6.1 years ago • Tears

Hi all, I have merged a number of WGS VCF files generated from the standard GATK pipeline with vcf-merge function of VCFtools. The merged

vcf-merge

updated 5.7 years ago • boymin2020

Good morning, I have a question about how to merge Seurat objects. My Seurat objects are from separately integrated datasets using Harmony. The reason for performing...the data size is too large and cannot be integrated effectively as a single dataset. Now, I want to merge these objects together. However, I have encountered a failure, and my error message is: testMerge <- merge(other…

merge

updated 11 weeks ago • Long

Hi, I have 90 VCF files which I am looking to merge into one VCF file. I am trying to use VCFtools to merge these files. For that I am following the below process but while using...vcf-merge command is not able to merge files. Please suggest the better way to merge these files. Install vcftools Install bgzip...Commands:::::::: bgzip -c file.vcf > file.vcf.gz tabix -p vc…

VCFs GWAS genome

updated 3.2 years ago • Manoj

path. Please help me to fix the three problems followed and give me some tips or directions to merging VCF files. Thanks in Advance. (1). When I want to merge the three example VCF files, I failed. commands: merge-vcf merge-test...2). Then I tried to compressed them. After I compressed and indexed the VCF files, I still failed to merge them. bgzip merge-test-a.vcf bgzip merge-test-b.vcf bg…

vcftools vcf merge

updated 3.9 years ago • Jianfengmao

Hello everybody, I should be grateful if you would kindly help me de fix my problem. I have a table like that : Chromosome start end info1 info2 chr01 1 100 15 35 chr01 150 300 15 39 chr01 299 750 16 39 I would like to merge the intervals that overlap ( line 2 and 3) and those that are closest (line 1 an…

merge bedtools

updated 11.7 years ago • Mchimich

Hey guys, So I'm working with pair-end data and I'm concerning regarding the merged/not-merged reads. I'm currently merging them using PEAR and QIIME 2, but I would not like to discard those not merged reads...Or it is best to discard them? I'm worried I'll loose too much information if I simply discard not-merged reads. Thank you

assembly

updated 4.9 years ago • las996

Hello, I am trying to merge multiple vcf files. I have seven vcf files with 50-60 samples each. I tried: bcftools merge file_1.vcf.gz file_2.vcf.gz...of individual vcf files. Is there anything wrong in what I am using or is there any better method to merge multiple vcf files? Thank you

SNP

updated 2.9 years ago • evafinegan

after double the bam. I have one bam file (1.bam), copy paste it (name it 1copy.bam), then merge 1.bam and 1copy.bam by using picard-tools MergeSamFiles. I use samtools flagstat check all the numbers are doubled...The question is 1, why the merged bam size is not doubled? 1.bam is 79Mb, but merged bam is only 84Mb. 2, I run the EstimateLibraryComplexity for 1.bam and...merged bam. the READ_PAIR…

merge picard tools

updated 7.7 years ago • Joe

Dear all, I have a set of samples each having multiple lane's replicates. When shall I merge the different replicate? BEFORE (that is, merge the fastq files) or AFTER (that is, merge the BAM files) the alignment? Does...the step of merging varies if the study is WGS or RNAseq? I haven't found a straight answer on Google, so I am asking. Thank you

alignment next-gen

updated 5.9 years ago • marongiu.luigi

files. it's paired end so there are 4 R1 and 4 R2 files. I would like to know when and how should I merge them? if i merge the fastq i can do a cat file 1 2 3 4> newfile ? but if I merge the fastq to make a single R1 file and a single R2

genome merge NGS fastq

updated 3.3 years ago • quentin54520

I have 10 bed files extracted from GEO Database, I want to use bedtools merge option to merge bedfiles and combine overlapping or “book-ended” features in an interval file into a single feature. But...after using bedtools merge the output file generated is reduced to just 4KB which earlier was approximately 1.6GB(all 10 files), am I using bedtools...merge correctly or is this an error

bedtools

updated 15 months ago • Amisha

Hi, I'm trying to merge these two bam files and I did the command samtools merge merged.bam file1.bam file2.bam However, it gives me this error

bam merge

updated 21 months ago • jyu429

I want to merge 2 gtf files in the same way that bedtools merge would do so. so that each overlapping region indicated by the coordinates

gtf merge

updated 8.0 years ago • melissa.ilsley

to generate an input normalized IP bigwig file. Since I have 3 replicates of a treatment file can I merge this three to increase my signal intensity ? Also , I received multiple fastq files from my core and I merged them using...cat *fastq.gz >> combined-In1.fq.gz I later realized that people use bedtools merge to do this, is there a formatting problem if I used cat ?? Thanks

ChIP-Seq deeptools bigwig merge

updated 7.7 years ago • ATCG

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

next-gen sequencing SNP genome

updated 3.5 years ago • mkamranazim

Hi everyone, I am trying to merge two EIGENSOFT dataset: - 1240K from [here][1] (version 42.4): contains 6676 individual / 1233013 SNPs - Human Origins from [here...2] (from Lazaridis et al. Nature 2016): contains 2068 individuals / 621799 SNPs However, when I merge it, using the build in mergeit function of EIGENSOFT package, I end up with a dataset with: - 8744 individual (6676+ 2068 s…

EIGENSOFT merge aDNA Population genetics

updated 3.3 years ago • yolek64754

Hi, I was wondering if anyone know how to merge 2 or more gff files to make a consensus gff file? I have gtf file from tophat/cufflinks pipeline gff file from velvet assembly...and i would like to merge these two to the already annotated gff file. The idea is to have one gff file instead of three gff files so that i can load

gff merge

updated 4.9 years ago • upendrakumar.devisetty

from different group of the experiment. I need to do assembly using StringTie software. Should I merge file first, or I can do it one by one. And what is the advantages of merging them. I tried to merge them but it give me error that

bam assembly lncRNA

updated 3 months ago • walaa.shalan

Hello! I would like to merge all amino acid sequences with identical names in a given fasta file (trimmed alignment). I know that this can be done for

alignment sequence

updated 6.4 years ago • jan

I'm trying to merge two vcf files, however i receive an error message vcf-merge SNPs_AXL_Australian_m.vcf.gz SNPs_AXL_Australian_w.vcf.gz...HASH(0x7fe63b12fd30)') called at /Users/lucashenriquesviscardi/Downloads/vcftools_0.1.13/bin/vcf-merge line 464 main::merge_vcf_files('HASH(0x7fe63b82bea8)') called at /Users/lucashenriquesviscardi/Downloads/vcftools_0.1.13...bin/vcf-merge line 12 I t…

vcftools bcftools merge

updated 7.4 years ago • viscardi.neander

I have 10 folders, each containing a bam file and a corresponding bai file. I need to merge the bam files, which I believe I can do with `samtools merge merged_filename.bam *.bam`. My question is that do I need to also...merge the corresponding bai files as well? And if so, should I just do - `samtools merge merged_filename.bai *.bai

bam RNA-Seq

updated 6.6 years ago • c_u

I used two lanes on a flow cell for the same library. I have the fastq files now, and want to merge the data together for each duplicate sample. At what point of the downstream analysis should I merge the two, and what

ChIP-Seq fastq merge two lanes

updated 7.0 years ago • addilynn.beach

issued the following command: tophat2 -p 32 -o fur1 -G NC_000000.gtf NC_000000 ../Trimmed_Reads/merged/fur1_unmerged_BB_PE1.fastq,../Trimmed_Reads/merged/fur1_unmerged_BB_PE2.fastq ../Trimmed_Reads/merged/fur1_merged_BB.fastq...Thinking that first feeding the non_merged PE and then the merged PE should be no problem. Note, merged PE should be treated as SE. I get the following log: ``` [20…

merged NGS tophat2 bowtie2

updated 22 months ago • apelin20

I'm getting an error when i attempt to merge 3 vcfs with VCFtools' vcf-merge function. See below: COMMAND: /ifshome/vcftools_0.1.10/bin/vcf-merge *.vcf > combinedVCF.vcf...perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /ifshome/vcftools_0.1.10/bin/vcf-merge line 9. BEGIN failed--compilation aborted at /ifshome/pbhatt/vcftools_0.1.10/bin/vcf-merge line 9. What is the…

vcf vcftools

updated 3.5 years ago • Sheila

primers, quality trimmed, and interlaced the forward and reverse reads. I now have a single fasta (not fastq) file with the following structure: >NS500647:208:HYKFFBGX2:1:11101:9580:1154 1:N:0:GATCAG GTGGTCAGCAGACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACAGATTTCAGGG...HYKFFBGX2:1:11101:24675:1156 2:N:0:GATCAG CGCACNNNATATGGGTTTTANTGGNGCAGCAT Is it possible to merge the R1 …

RNA-Seq

updated 5.4 years ago • O.rka

I have 30 + bam files and I have merged the data using samtools merge(adding RG tag using -rh option).I ran mpileup on each of the .bam files separately and ran...mpileup on the merged data to look at average coverage.Say if I have 10x average coverage in each of my individual samples,I am expecting...a coverage of roughly 10x*n in the merged case where n is the number of samples .However,I see m…

samtools coverage bam

updated 8.2 years ago • Kssr

Is the stringtie's merge used to merge the transcripts fronm biological replicates prior to differential expression analysis

RNA-Seq

updated 6.5 years ago • amy16

sample, sequencing machine and everything is the exactly the same, are the bam file which is merged after mapping and pre-merge fastq file, then mapped bam file same?? 2. And if they are same, can I merge bam files using samtools

sequencing bam merge

updated 6.2 years ago • woongjaej

Hey everyone , i have two fasta files having same header with different sequence content. i have to merge both files. i want to write a script in perl or

fasta

updated 15 months ago • skdv2522

Hello, In order to perform population gnomic analysis, I am trying to merge many and huge variants data (gVCF), such as several dozens Gb, over 20 files. Bcftools merge and vcf-merge were used so far...but very slow to merge those files into just one file. Do you have any ides to merge huge gVCF files? I want to use variants as many as possible so

gvcf vcf merge

updated 2.9 years ago • ymat

of individuals that are related to some individuals inside the file I just mentioned. I want to merge both files. The file I want to merge to the first file is this one: `ALL.chr1.phase3_shapeit2_mvncall_integrated_v5_related_samples.20130502.genotypes.vcf.gz...I tried to merge them using the following command: ``` vcf-merge \ ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.v…

merge PED VCF

updated 15 months ago • MMK

fa,.fasta} [...] Warning: cannot find genomic sequence file /data/reference/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/HG1007_PATCH...fa,.fasta} Warning: cannot find genomic sequence file /data/reference/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/HG1032_PATCH...fa,.fasta} [...] Warning: cannot find genomic sequence file /data/reference/Homo_sapiens/Ensembl/GRCh37/Seque…

cuffmerge fasta

updated 10.9 years ago • jobinv

12,241 results • Page 2 of 245

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