Bfast Match Paired End Reads - Reports Half Total Number Of Reads
I'm using bfast 0.7.0a and testing on the paired end data present in the bfast user manual (Figure 5.4 in bfast-book.pdf). The format for this fastq file is shown that paired reads should follow...
View ArticleHigh level of duplicate in one reads of paired-end data
Hi,We are doing some transcriptomic analysis on bovine immune blood cells and we seem's to have some problem with high levels of duplicate in our data. Our library were prepared with the illumina...
View ArticleTophat - Understated Number Of Reads In The "Align_Summary.Txt" File
Hi all. I'm working with paired-end rna-seq data to assemble transcriptome of my species of interest. I've just realized that Tophat is understating the number of reads that I actually have and...
View ArticleDealing With Read Counts Under Pe And Se Scenarios
Hi, I am unsure how to deal with this case to go about analysing RNA-seq data. Suppose that you have a control and treatment setup with 4 biological replicates each. However, two in control and two in...
View ArticleHow To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific
I've been provided with more than a billion reads of RNAseq data for a poorly annotated nematode species. They appear to be 2x100 paired-end Illumina reads – I currently know frustratingly little about...
View ArticleWhat Better Way To Get The Paired Reads Aligned Against The Reference Genome?
Hi everybody,I have a group of paired reads sequenced using Solid 4 (50bp each mate). I discovered that reads are contaminated by E.coli. My strategy is to align the reads against the reference genome...
View ArticleBest Cnv Software?
Hello,I know there are many reviews out there, but I can't seem to find exactly what I like.I found this software called mrCaNaVaR, and it's great since it has it's own aligner which is supposed to be...
View ArticleHow To Convert A Soapsnp Output File To Soap, Sam Or Bam Formats
Hello,I would like to know if there is any tool to convert SOAPsnp to SOAP? Once it is converted to SOAP, I can convert it to SAM using Soap2Sam from reseqtools. Hopefully using reseqtools is not that...
View ArticleHow To Interpret Crossbow Data
Hello,May I know how to interpret Crossbow output. Is there any chance of building a SAM or BAM file from Crossbow output. I am looking into genome mapping. I know there are many tools available for...
View ArticleTrimming Adapters For Paired-End Sequences
Hi all,I got illumina paired end fastq files. They told me to trim read 2 at the beginning for ~20 to 30 bp due to the WGA adapters. Can we find the adapters by looking in to the quality? Which tool is...
View ArticleAmos With Paired End Data
Hi all, how do I take advantage of paired end data with AMOS? I have a 2x100bp fastq file that I would like to use AMOScmp-shortreads with. I see that when I google for it, there might be a .mates file...
View Articlejoin non-overlapping paired-end reads
I have a batch of illumina paired end reads with a shorter than anticipated reverse sequence for a ~550bp amplicon.The joining tools which I have used before (i.e. USEARCH, ea-utils) talk about merging...
View ArticleResampling Fastq Sequences Without Replacement
Hello, I want to extract a random sample (without replacement) of 7.5 million fastq sequences from illumina sequencing data that contains about 30 million sequences each in of the reads. I want to...
View ArticleGsnap: How To Output Only Alignments With Minimal Number Of Mismatches?
I am aligning paired-end ChIP-Seq data of drosophila transcription factors.I would like to have a .sam file with the following alignments reported: - A maximum of three mismatches, i.e. three wrong...
View ArticleMapping Trimmed Paired End Reads With Mapsplice
Hi! I'm trying to map illumina paired end using MapSplice. I used script named sickle to trim the bad quality tails and the output looks like this:Paired end 1@TUPAC_0006:1:1:3062:1473#0/1...
View ArticleAlign Paired End Reads Using Blast
Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the reads which were not mapped by gsnap. It seems that BLAST can only...
View ArticleDoes Every Read In Paired-End Sam File Have The 0X0001 Flag?
Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?...
View ArticleFastq Sort By Sequence
Dear all,I have some questions about manipulating fastq files. Its the first time I do this, so I want advice, how to do it. Its a special case, because I only want to keep reads when the following...
View ArticleMapping target-enriched reads to a transcriptome reference
Hi all, I have carried out transcriptome sequencing on a plant species and then, from the resulting assembled contigs, have designed capture probes for 970 gene regions. I then carried out...
View ArticleMacs Raises Error: No Such File Or Directory
I am trying to run macs14 with sam files from paired-end data + control. Macs14 returns "No such file":sb7904313:line2 $ macs14 -t /Volumes/Data/G6L2_G6L3/s5/clean_paired_sample.sam -c...
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