Hi all,
I'm trying to map 2 X 100 PE Illumina reads (transcriptome) back to a small number of contigs. I want to get the number of reads that align to each contig as quickly as possible. Here's the commands I've tried so far but it isn't working.
Here's the errors I get:
The problem seems to be once the samtools apps start running. I'm using samtools version 0.1.19-44428cd. Any ideas on what I'm doing wrong? Is there an easier way?
Thanks!
Kevin
I'm trying to map 2 X 100 PE Illumina reads (transcriptome) back to a small number of contigs. I want to get the number of reads that align to each contig as quickly as possible. Here's the commands I've tried so far but it isn't working.
Code:
SCAFFOLD_INPUT_FILE=test_selected_sequences.fas S1_FASTQ_INPUT_FILE=D13F4ACXX_s6_1_GSLv2-7_32_SL18114_test.fastq.gz S2_FASTQ_INPUT_FILE=D13F4ACXX_s6_2_GSLv2-7_32_SL18114_test.fastq.gz REF_MAP_BASENAME=test BWA=`which bwa` SAMTOOLS=`which samtools` BCFTOOLS=`which bcftools` VCFUTILS=`which vcfutils.pl` BT2=`which bowtie2` BT_BUILD=`which bowtie2-build` TDSTAMP=`date | awk 'OFS="_" {print ($2,$3,$6,$4)}'` ${BT_BUILD} ${SCAFFOLD_INPUT_FILE} ${REF_MAP_BASENAME} ${BT2} -x ${REF_MAP_BASENAME} -1 ${S1_FASTQ_INPUT_FILE} -2 ${S2_FASTQ_INPUT_FILE} --qc-filter --no-unal -S ${REF_MAP_BASENAME}.bowtie2.mapped.sam $SAMTOOLS view -bT ${SCAFFOLD_INPUT_FILE} ${REF_MAP_BASENAME}.bowtie2.mapped.sam > ${REF_MAP_BASENAME}.bowtie2.mapped.bam $SAMTOOLS sort ${REF_MAP_BASENAME}.bowtie2.mapped.bam ${REF_MAP_BASENAME}.bowtie2.mapped.sorted $SAMTOOLS idxstats ${REF_MAP_BASENAME}.bowtie2.mapped.sorted.bam
Code:
[samopen] SAM header is present: 28 sequences. [bam_index_load] fail to load BAM index. [bam_idxstats] fail to load the index.
Thanks!
Kevin
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